Hi there. I have the mats from MFT:
Die-namics Embossing Pad Combo , but I am thinking they are probably the same as the PTI mats. You can take a look at the link above and see if they are the same.
I use the thinnest mat that comes in the set and I don't alter my stack at all. I use the platform all the way closed, the 2 clear cutting pads, and the thin embossing mat in between with the paper and Die-namics. The thickest pad won't fit in that stack, so you'd have to probably open one of the tabs on the base platform, but again, I don't use the thicker one, personally.
I hope that helps.
I'm a designer from MFT and I love MFT Die-namics (all of them).