Actually, the first sync is the only one that should do that.
When you delete apps from the iPad, they will stay off. Same for the iPhone.
Go into iTunes with your iPad connected, select it from the Devices list, and click on the Apps link at the top of the screen. Now uncheck all the apps you don't want on the iPad, and sync again. Those apps will be removed and should not sync again unless you go back and check them.
There is still a tendency for apps that you download on one device to get synced to the other, if compatible (which almost all are for the iPad). This is infrequent enough that it is no problem just to delete them as they occur.
If you do set up two separate accounts for the iPad and iPhone hold in mind that you are going to the opposite extreme. If you want the same app on both devices (and some universal apps do work well on both devices) you will have to pay for them twice.
If you go into your iTunes preferences the Devices tab, and turn off auto-sync, you will gain a little more control over when the devices sync. This will give you the opportunity to tailor a sync before it happens.
