So how many partitions did you create and what sizes? The phone will only see the first partition as the regular SD card, so if you took an 8GB card (which really has about 7.5 GB capacity) and added a 4GB second partition then a single partition of about 3.5 GB is what the phone would see. If the phone has an init.d script that supports moving apps to SD, or you have an app like Link2SD, then those can use the second partition, but the normal system menus won't see it.
As for your missing apps, did you move these apps to SD before partitioning (using the system menu, if your android version has that, or maybe an app with root privileges such as Link2SD)? If so, did you back up the card before partitioning, including hidden files and folders (especially the folder .android_secure)? Partitioning is almost always a destructive process, so anything that isn't backed-up before partitioning is likely to be lost, and that would include any apps that had been moved to SD that way.