First, go into iTunes Preferences, the Devices tab, and prevent auto-sync. This will keep you from accidentally syncing the iPad until you are ready (or accidentally click the Sync button in iTunes). You can turn it back on later if you want.
When you connect the iPad and it offers to sync, choose Transfer Purchases if it is offered. If not cancel the dialog, right click on the iPad in the Devices list and choose Transfer Purchases.
When it is done go to the Apps page and make sure all your apps are present, and checked. If they are not both present and checked they will be removed when you sync.
I am not certain how it will handle Cydia apps, so be extra careful and make sure those apps have been transferred and have checkmarks.
Also keep and eye on the home page layout in iTunes. If it does not look like what is on your iPad try a backup (same place as Transfer Purchases).
It's a good idea to check all the other sync options too, to make sure they are set the way you want. If you've been syncing nothing, leave them off at first. You can try adding each section one at a time later, as needed.
Transfer Purchases will also copy all other iTunes purchases to the computer; such as music, iBooks, etc. It will (probably) not transfer stuff you added manually though email or other apps.