Talk to your bodyshop that is doing the painting. Discuss and decide on the color you want and where they buy their paint. Then go to their paint suppler and they can make up a can or two of spray paint in that same color for you. Not cheap but that would solve your issue.
When I went to Autobody School way back in High School, we were taught to paint any place that is hidden behind fenders, hood, trunk and the doors, reassemble, adjust then paint. This way you would have less chance of damaging your paint.
Later when I worked in a shop, we even went as far as painting behind some of the trim pieces, particularly body side mouldings when they were attached to the body with clips (not the 3M adhesive type). You did have to do a real good job of masking those pieces.
