The best way I have found to prevent modules from overridding other modules that I have installed is to check the files themselves.

If...

/thisfolder/thatfolder/blahblah.php

is a file that is used in both modules then I look at the one that is not currently installed and check to see what it changes in comparison to:
1. the orginal zen-cart file of that name and location and,
2. the currently used zen-cart file of that name and location.

I have generally found that payment option modules rarely upset other payment modules, however, most modules are written to be an improvement over the base zencart install. Hence, they do not, nor can they really, take into consideration every single different module out there, past, present and future.

Most importantly....BACKUP BACKUP BACKUP....Oh and did I mention BACKUP!

Backup your files and your database prior to installing any new modules! I have had to kick myself in the before, for not doing that.