If your wanting the snowman type rig, then usa a same size bottom sinking bait as the pop up bait. This normally cancels each other out to a certain degree to create a critically balanced bait. Ie easier for the carp to hoover up into its mouth and move more naturally in the swim.
Sometimes when you test your rig in the margins you may find the pop up bait a little too bouyant and gives more of a pop up effect as apposed to a critcally balanced bait.
A piece of shot on the hair will usually help if this happens, or alternatively a piece of rig putty on the eye of the hook and top of shank will work equally well.
Ive tried squeezing my pop up boilies to make them sink and have never had much success that way.
If you dont fancy using shot or putty, use a slightly smaller top pop up bait than your bottom bait and that should work too.
Just keep experimenting and find which works best for you.