4
You shouldn't have to make any changes to mainfile.php unless you plan to change your database or move your site to a different URL.
The site you pointed out just uses a modified version of the x2t theme. Most of your modifications to colors will be in the CSS style sheets that accompany your theme. To edit image placement, and hard-coded features, you'll need to edit the theme.html file that accompanies your theme. The easiest way to change logos is to navigate to the images folder of your theme and look for the logo (usually logo.gif or logo.jpg), then overwrite it with your own custom logo. You may want to replace the default logo in the {xoops root}/images directory as well, but be careful of sizing as this can throw off layout.
I use Studio MX 2004 and text editors for all my coding/designing needs and I've yet to have a problem with it.
The best thing you could do would be to download XSAS and practice locally. That way you can tinker away without worrying about what your site's visitors see. Then, when you have the look you want, upload the files and new database schema.
You can find a tutorial on how to develop your site locally here:
https://xoops.org/modules/newbb/viewtopic.php?topic_id=18687&forum=7#forumpost79519
This is all assuming you want to go beyond just installing someone elses theme. As mentioned by limecity, basic customization just requires uploading some files and making a few clicks.