I wouldn't worry about your puzzle joint.  Personally, I don't pre-coat the ends before assembly, although other builders may have a good reason to do so.  They're usually a pretty tight fit anyway and would scrape off most of the epoxy as you fit them together.  I feel that assembling first and them brushing on the epoxy gives me a chance to check how flush the surfaces are beforehand.  And the subsequent brushing on of the epoxy does bleed through pretty thoroughly, as you noticed.  

Thanks.  I precoated the next set of joints and it was quite a bit messier process overall. Also more clean up to do with the joint afterword with the amount of epoxy that ended up being pushed thru as you noted, as well as any further bleed through. As I get to understand a bit more working with epoxy two things are becoming clearer: tidy and less are better than messy and more. Went back to dry fitting for the last join, just ensured the joints were well coated to ensure more consistent penetration. Will see the results tomorrow but am more confident in the result.