If you need ground chipotle, try this link:
http://www.penzeys.com/cgi-bin/penzeys/ ... potle.html
I’ve bought many spices from them; the quality of their products is excellent.
As far as the rub, you can use ground chipotle whenever the recipe calls for chili pepper. I would cut the amount to half chipotles and half chili pepper, because it has an intense smoky flavor. I would rather get the smoke flavor from wood (that’s my own preference). Check the posts under “Chipotles” for more ideas.