I put the coins back in before I put any finish on. Since you are applying your finish by wiping you can put a little on the coin but not over do it. Too much finish on the coin can sort of make them lose the sharpness of the intricate little details.
I use water based poly as a first layer on oily woods to fill the pores, as oil based poly looks terrible unless the wood is sealed first. I will lightly sand and then switch over to oil based polyurethane wiping it on with a small piece of cotton cloth from an old shirt. I have experimented with water based on my 62 Kodiak Special this past summer and ended up sanding most of it off. The bow just started looking crappy the more finish that I applied, so I went back to the oil based and it turned out to be one of my prettiest restores. Here is a link to a thread on that bow:
http://tradgang.com/cgi-bin/ultimatebb.cgi?ubb=get_topic;f=14;t=006928 Have fun and share some pictures as you go. I am working on three bows presently that belong to one of the fellows on here. Let's just say that they were a challenge but the worst is behind me. In a couple of weeks I will start a new thread on that rescue effort, just a bit busy at the moment and it takes forever to load pictures on this site.