I haven't had any issues with sending MMS but have seen issues with a few different Cyanogen set ups. This was posted by Conap over at XDA for his rom, but maybe it would work with this one. Do a Nand Backup first just to be on the safe side, but I really wouldn't think this would cause any issues. It should either work or not, and not break anything important...
HTC Droid Eris ROM Site
Once there - look for the Cyanogen 2.5 MMS fix.
As far as the messages going through both stock and Handcent, there are a couple of ways. Go to Settings > Manage Applications > Message App > Clear Defaults. Then go to send a message and it should ask you which one you want to use, make sure you check the button that asks if you want this app to be used as default. Or, you can just delete the stock app. Use something like Titanium BackUp so you still have it if you want it.
Hope this helps...