Friendly URLs - not working, how do I troubleshoot?

right.. this is just while setting up the MODx of course.

I thought a little bit about what you said, and came to the obvious realisation:
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]

so of course, going to the index page. Having changed that to default.php (my MODx index,) things seems to be working.

I would recommend doing it the other way around (leaving index.php as the MODx index file and making default.htm the index file for the other site) because some third-party MODx components could have that name hard-coded in.