I'm no expert for sure - but why not just use cauls to keep everything aligned?

Fine Woodworking has a nice article that demonstrates how to use them.

 

I think if alignment is your goal, the pocket screws will be less effective and more of a pain to use then simple clamping cauls. If you google this, you'll get plenty of recommendations to help with your glue up.

Also, make sure you're using the right clamps. It's not that f-style clamps can't work for this application, but it's certainly easier using parallel or pipe clamps, or some of those aluminum channel panel clamps HF sells.

 

Part of the difficulty of using pocket screws is keeping the boards aligned since the screws go in at an angle, so as Dustin said, it'll make the glue up harder.

I third the clamp and caul suggestion.

 

As the others noted, the pocket screws will work against you. They will cause a glue up to "barrel".

 

There's some debate about the "salt trick",
which is where you put salt in pva glue to
prevent slippage as the clamps are tightened.

Some say it works and others say it makes a
weak joint. I was going to try it myself but
haven't yet because of the debate.

One thing I have done that works well is to
put in little wire nails and clip off the heads.
Then as you tighten the clamps the nails
keep the parts in alignment.

 

I use c-clamps on the ends and a dead blow to correct any center misalignment, always worked for me but cauls are probably the best solution.

 

Down around 12 to maybe 18 inches clamps on the ends of the joints are fine if your boards are flat. If the joints are longer, or if you're alternating the wood to eliminate a slight bow, cauls are really needed.

I made a caul template out of 1/4" MDF and gave it approximately a 1/16" rise per 12" run on the edge. I then used it with a flush trim bit to make a couple dozen cauls of three different lengths and added red vinyl stucco tape to the curved face so they don't get stuck in the glue.

They work great with F clamps on the ends of them. Perfect glue ups.