Apps like CyDelete and SBSettings dont have an icon, so when you try to look for them on your SpringBoard(where all your apps are located) they wont be there.
Say you install WinterBoard, well Winterboard has an icon with it (as well as a 'hidden' app inside the settings.app if you choose to hide it. Now after installing WinterBoard, you can download CyDelete and then activate the moving icons feature and you'll notice WinterBoard has a feature to be deleted, which unlike originally you would have to go into Cydia, wait for it to load, and uninstall the package.
Now if your downloading and installing cracked packages, or packages from a repository that was added manually, sometimes they forget to have you reboot and reinstall when downloading a package.
If your apps, likes WinterBoard, AutoSilent, BiteSMS, and others are still not showing up, you might be better off restoring your iPhone and rejailbreaking.