Two devices, one iTunes: How do you prevent apps from transferring

You can copy apps (and other iTunes purchases) from your iPad to your computer's iTunes via File > Transfer Purchases.

To select which apps to sync to the iPad, connect the iPad to your computer and select it on the left-hand side of your computer's iTunes under 'Devices', and on the right-hand side there should be a series of tabs, one of which should be Apps - if you select that tab you can then select which apps (via the listbox on the left-hand side of the window) to sync to the iPad. If you don't want new apps to automatically sync to the iPad then make sure that the 'automatically sync new apps' tickbox under the apps listbox is unticked.

Syncing apps : http://support.apple.com/kb/HT1977 (the page isn't updated anymore but it looks to still be correct)

I have 'sync apps' ticked at the top of that tab, but not the 'automatically sync new apps' below the listbox - I also have an iPhone and that prevents new apps that I get for the phone automatically being copied onto the iPad when I next connect it, so only the apps that I have ticked in the listbox are on my iPad.

You should be able to tick the box at the top and then select from the list which apps that you want on the iPad - clicking 'Sync' at the bottom right of the window should then apply that selection to the iPad.