Ok, fixed it... The dom tree was changed after CodeMirror was loaded, so i moved the code from the jquery.php files to the js files (filemanager.js and templates.js). 
Here is how to implemented the hacks.
Template manager hack:Step 1: Add 
 $xoTheme->addScript('browse.php?modules/system/js/codemirror.js');  
 after 
 $xoTheme->addScript('browse.php?modules/system/js/templates.js');  
 in modules/system/admin/tplsets/main.php .
Step 2: Add 
 $xoTheme->addStylesheet( XOOPS_URL . '/modules/system/css/docs.css');  
 after 
 $xoTheme->addStylesheet( XOOPS_URL . '/modules/system/css/admin.css');  
 in modules/system/admin/tplsets/main.php .
Step 3: Change 
 function tpls_edit_file(path_file, file) 
{ 
    $('#display_contenu').hide(); 
    $('#display_form').hide(); 
    $('#loading').show(); 
    $.ajax({ 
        type: "POST", 
        url: "./admin/tplsets/jquery.php", 
        data: "op=tpls_edit_file&path_file="+path_file+"&file="+file, 
        success: function(msg){             
            $('#display_contenu').html(msg); 
            $('#loading').hide(); 
            $('#display_contenu').fadeIn('fast'); 
        } 
    });     
    return false; 
}  
 to 
 function tpls_edit_file(path_file, file) 
{ 
    $('#display_contenu').hide(); 
    $('#display_form').hide(); 
    $('#loading').show(); 
    $.ajax({ 
        type: "POST", 
        url: "./admin/tplsets/jquery.php", 
        data: "op=tpls_edit_file&path_file="+path_file+"&file="+file, 
        success: function(msg){             
            $('#display_contenu').html(msg); 
            $('#loading').hide(); 
            $('#display_contenu').fadeIn('fast'); 
            if(path_file.slice(-3) == "css"){ 
                var editor = CodeMirror.fromTextArea("template_code", {     
                    height: "350px", 
                    parserfile: "parsecss.js", 
                    stylesheet: "css/csscolors.css",                     
                    lineNumbers: true, 
                    textWrapping: false,  
                    path: "js/"                 
                }); 
            }else if(path_file.slice(-3) == ".js"){ 
                var editor = CodeMirror.fromTextArea("template_code", { 
                    height: "350px", 
                    parserfile: ["tokenizejavascript.js", "parsejavascript.js"], 
                    stylesheet: "css/jscolors.css", 
                    autoMatchParens: true, 
                    lineNumbers: true, 
                    textWrapping: false,  
                    path: "js/" 
                }); 
            }else{ 
                var editor = CodeMirror.fromTextArea("template_code", { 
                    height: "350px", 
                    parserfile: ["parsexml.js", "parsecss.js", "tokenizejavascript.js", "parsejavascript.js", 
                                "tokenizephp.js", "parsephp.js", 
                                "parsephphtmlmixed.js"], 
                    stylesheet: ["css/xmlcolors.css", "css/jscolors.css", "css/csscolors.css", "css/phpcolors.css"], 
                    lineNumbers: true, 
                    textWrapping: false,  
                    path: "js/", 
                    continuousScanning: 500 
                }); 
            } 
        } 
    });     
    return false; 
}  
 in modules/system/js/templates.js .
Step 4: Change 
 <textarea name="templates" rows=24 cols=110>'.$content.'textarea>  
 to 
 <textarea id="template_code" name="templates" rows=24 cols=110>'.$content.'textarea>  
 in modules/system/admin/tplsets/jquery.php.
That should do it for the template manager, the hack for the filemanager is almost the same but here's the guide for that 

...
File manager hack:Step 1: Add 
 $xoTheme->addScript('browse.php?modules/system/js/codemirror.js');  
 after 
 $xoTheme->addScript('browse.php?modules/system/js/templates.js');  
 in modules/system/admin/filemanager/main.php .
Step 2: Add 
 $xoTheme->addStylesheet( XOOPS_URL . '/modules/system/css/docs.css');  
 after 
 $xoTheme->addStylesheet( XOOPS_URL . '/modules/system/css/admin.css');  
 in modules/system/admin/filemanager/main.php .
Step 3: Change 
 function filemanager_edit_file(path_file, path, file) 
{ 
    $('#display_file').hide(); 
    $('#edit_file').hide(); 
    $('#loading').show(); 
    $.ajax({ 
        type: "POST", 
        url: "./admin/filemanager/jquery.php", 
        data: "op=filemanager_edit_file&path_file="+path_file+"&path="+path+"&file="+file, 
        success: function(msg){ 
            $('#edit_file').html(msg); 
            $('#loading').hide(); 
            $('#edit_file').fadeIn('fast'); 
        } 
    });     
    return false; 
}  
 to 
 function filemanager_edit_file(path_file, path, file) 
{ 
    $('#display_file').hide(); 
    $('#edit_file').hide(); 
    $('#loading').show(); 
    $.ajax({ 
        type: "POST", 
        url: "./admin/filemanager/jquery.php", 
        data: "op=filemanager_edit_file&path_file="+path_file+"&path="+path+"&file="+file, 
        success: function(msg){ 
            $('#edit_file').html(msg); 
            $('#loading').hide(); 
            $('#edit_file').fadeIn('fast'); 
            if(path_file.slice(-3) == "css"){ 
                var editor = CodeMirror.fromTextArea("filemanager_code", {     
                    height: "350px", 
                    parserfile: "parsecss.js", 
                    stylesheet: "css/csscolors.css",                     
                    lineNumbers: true, 
                    textWrapping: false,  
                    path: "js/"                 
                }); 
            }else if(path_file.slice(-3) == ".js"){ 
                var editor = CodeMirror.fromTextArea("filemanager_code", { 
                    height: "350px", 
                    parserfile: ["tokenizejavascript.js", "parsejavascript.js"], 
                    stylesheet: "css/jscolors.css", 
                    autoMatchParens: true, 
                    lineNumbers: true, 
                    textWrapping: false,  
                    path: "js/" 
                }); 
            }else{ 
                var editor = CodeMirror.fromTextArea("filemanager_code", { 
                    height: "350px", 
                    parserfile: ["parsexml.js", "parsecss.js", "tokenizejavascript.js", "parsejavascript.js", 
                                "tokenizephp.js", "parsephp.js", 
                                "parsephphtmlmixed.js"], 
                    stylesheet: ["css/xmlcolors.css", "css/jscolors.css", "css/csscolors.css", "css/phpcolors.css"], 
                    lineNumbers: true, 
                    textWrapping: false,  
                    path: "js/", 
                    continuousScanning: 500 
                }); 
            } 
        } 
    });     
    return false; 
}  
 in modules/system/js/filemanager.js .
Step 4: Change 
 <textarea name="filemanager" rows=24 cols=110>'.$content.'textarea>  
 to 
 <textarea id="filemanager_code" name="filemanager" rows=24 cols=110>'.$content.'textarea>  
 in modules/system/admin/filemanager/jquery.php.
The package is also updated (Still based on the code delivered with XOOPS 2.5 Alpha) :-p.
I hope it works and it will be included in the core.
Greets Dylian.
BTW, got the solution from this Google Groups post: 
http://groups.google.com/group/codemirror/browse_thread/thread/1a7a5f529eccc1a/a5928c35dff3ef80?lnk=gst&q=false#a5928c35dff3ef80