Dave,
Thanks for the quick reply, and for your incredibly explicit directions in the pdf. I feel a bit like an idiot asking more of you but, I did get stuck in your directions very close to the end at the "Source Contraints" step. I found the .tcl file, but I'm not sure how to source it and I assume once I do that successfully the following line of code will work, but at the moment it does not for me. I also tried your autogeneration thing, but quartus 12.1 threw a bit of a fit. I would rather step through it instead of auto-generating though, so I'm more interested in what you meant about those constraints.
Some comments I noticed:
Everything I've seen always has a DMA block connected to the pcie block. Since my data transfers are relatively basic, I was wondering if that was really necessary (I've read DMA has a large overhead, and so is not efficent for small amounts of data).
From a curiosity standpoint, is there a way to configure this thing without having to use the host PC? Isn't there a way to find the PCIe addresses without just finding it on the host PC? I thought my idea of polling the physical addresses wasn't the worst thing...
And as a more general question, is the purpose of this whole thing to have something like a PCIe block that just has a more basic interface (tx/rx) kind of thing to be used in other designs?
Thanks so much for your help thus far,
Craig