This is how to do everything via ClockworkMod Recovery. Before you do anything I would reflash ClockworkMod Recovery through Rom Manager, just for the hell of it. That could be part of the problem.
Make a backup-
Power off your phone. Then slide open the keyboard and hold X and Power at the same time. Once the Motorola icon comes up you can let go of Power but keep holding X. It will come up with a black screen with Green letters and say ClockworkMod Recovery at the top. Scroll down to Nandroid using the volume buttons. Once on Nandroid, hit the Camera button to select. Go to backup and hit Camera button again. It might have a bunch of "No's" and one "Yes", just scroll down to yes and enter. Let it do its thing. Once it's done, hit the power button to go back to the main menu. From there you can reboot the phone or continue flashing a rom. To restore a backup, do the same thing, but instead of selecting backup, you'll hit restore.
Flashing a rom-
Find the rom you want via Droid Forums. Download the rom to your computer. Do not unzip or rename or do anything to it. Move the download to the desktop on your computer. Plug your phone into the computer, pull down the notification bar and select USB connected to transfer files from your computer to your phone. A box on your computer should pop up. Select open folder to view files. When it opens you should be able to see everything that's on your SD Card. Drag and drop the rom directly on your SD Card, make sure it's not in any folder!!! Once it finishes transfering the information you can unplug your phone. Power off and boot into recovery like you did to make a backup. First, do a factory reset (wipe data and cache), then go into the partitions menu and format boot, then format system, then go to the advanced menu and Wipe Dalvik Cache. Press the Power key to get back to the main ClockwordMod menu, scroll down to install zip from sd card, then choose zip from sdcard, then navigate to the directory where you stored the ROM zip file. Select the file and watch it install! After this, press power to get back to the main menu and select reboot. Once it boots up you can try to use Titanium, or just wait for Google to install your apps. You will have to activate your phone and sync your accounts but it doesn't take long. It's basically like starting with a new phone. A second reboot once everything is done is recommended.
You would basically do these same steps for kernels unless you use rom manager.
I know it sounds like a lot, but it's very simple and actually a lot of fun learning this stuff about your phone (for me anyway, lol). Let me know if you have any questions!