1. If the slots are exactly identical and this is sort of a "one off" project, then you might use Assembly Features -- use the "Features" tab in Assembly and cut the slots through everything at one time.
2. If you already have the rail and want to "copy" the slots onto the base. Then assemble them together. Then, double click on the base to edit in context. Then either do an "Include Edge" or "Interpart Copy" to get the edge or face from the rail copied over (associatively) to the base. And then just use that to cut the base.
Dan Staples Director, Solid Edge Product Development