I took off the brakes... replaced the driver side and then on the passenger side I notice the old inside pad had the Clip on the bottom, but the one I'm replacing it with had the clip on the top.

So I've must of did the same thing on the driver side. I didn't feel like redoing it. So now the inner pad clips are on the TOP, but the old ones had them on the bottom, if I swapped the sides it should be on the bottom.

I'm wondering if it matters? They are sqeaking... but I'm just hoping it's the break in period.

 

I cant remember exactly, but the clip I think you are referring to is the "squeaker." It should drag on the rotor when the pad becomes to thin. It should in theory pull "apart" and not "compress" into itself, i.e. it should drag away from it's mounting point so it can make the noise under normal forward driving. I hope this helps, sounds kinda of confusing even when I read it to myself.

 

Also I don't recall new pads squeaking.

 

Is this the first time your brake pads have been replaced? Because it actually sounds like your inboard brake pads are now in the right orientation, and they were in the wrong orientation before you replaced them.

I remember the indicator tabs originally being on the top, like in this diagram from the shop manual.

 

thanks. These have been changed before.. but the 1st time doing them myself.

 

The drawing is correct showing the wear tab on the inner pads at the top.
Sqeaking likely is from the pads moving against the pistons. Your kit should have had a little pouch of hi temp lubricant ti put on the back of the pads. Just a thin film, not a big glob. You don't want it on your pads.
And make sure the pads are just a little free in the calipers, just a tad.