"I'm confused. A song I'm practicing says to capo on the first fret which will change one of my chords to E and D. How do I play these chords if my capo is in the way?"

I'm not sure why people are giving answers to questions you aren't asking. It's probably because you resurrected a thread with another question and folks haven't caught on to this being an old thread.

Mudcatters don't read whole threads. They read the first post and reply to it. Because of this, no matter how related you may think a question, if you really want an answer, it's best to start a new thread -- even if you think it's redundant.

As to your question...

..I'm guessing, because your question is unclear, that you are having trouble because either the music that is telling you to play with a capo on the first fret is still referring to the chords by their shape than by their capo-altered key. If that's the case, when it says to play an "E" or a "D", it merely means to play that shape -- thinking of the capo as the nut (such that the second fret is now the first fret).