Talk about doing your homework - way to go!
I recommend making a nandroid after this one of your entire phone, copy it to your PC, and then you can delete that one from your SD card after you're comfortable with the whole process. Typically you'll just be replacing /system and /data when you flash other roms.
With Titanium, make a backup of all user apps and data and all of the Sense goodies that matter - especially your browser, mail and sms data. To be perfectly honest, I usually screw up that last part myself, so SMS Backup or MyBackup Root, free in the Market, saves me there.
Next - use Titanium to freeze bloatware - Spiderman, that game controller thing at the top of the app drawer - any of the junk you won't be using.
Myself, I'm running the stock rom, with some bloatware frozen and the kernel from netarchy - I overclock from time to time, and I have working full copy of Ubuntu 9.1 (Linux) that I run side by side with Android. But that's me.
Once you have a good baseline of backups, you're ready to play around with any customizations or roms that sound interesting to you.