Ok, we'll start at the beginning. You flash the kernel to give you root access, and some addons and fixes (Overclocking, which you've experienced, and undervolting are a couple).
ROMs add on some things, and apply more fixes (JIT, 3D gallery, live wallpapers etc.)
Themes change the look of your phone. Sometimes they come with a little bit of stuff like widgets and apps.
You put these in /sdx/zip on your sd card, boot to custom recovery, clear the dalvik cache (under advanced options) and flash the zip.
My favorite apps include:
ADW Launcer Ex
Xscope web browser
Cachemate (root required)
Titanium Backup (root required)
Wifi Thether (root required)
There are many, many more but these are just the ones from the top of my head.
Oh, and I almost forgot!
Before you flash anything, it's a good idea to deodex. You can deodex manually but its laborious. You can just flash the file here:
EB28 Stock theme template (deodexed)
make sure to follow all directions. AND DON'T FORGET TO CLEAR THE DALVIK CACHE!!!!!!