I agree. It takes some time to get used to focusing both lens correctly.
I use following technique: for close-ups I just focus both lenses all the way down and fine tune via taking lens focus.
For focusing on far objects everything is vice versa, except for fine tuning is done again with taking lens.
For inbetween distances I try to focus both lenses on approximately same distances basing on focusing marks on 'em.
Wish you luck and lots of patience while practicing.