2
you are thinking way too complicated...
the whole thing is very simeple.
and forget about the mainfile.php ..
you don't need to bother about that file as long as your XOOPS is fine..
Now step 1.
Go to your system administration
then click on system admin
click on perference
from there you see THEME
select any theme from there
and submit then your site will have a new skin
If you have a custom theme,
copy it to your
http://wwwt.yoursite.com/theme/(only if your XOOPS is at your root.
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changing logo will only require you to replace the current logo in the theme folder
then edit the rest accordingly.