When you have the pattern length set to 3 beats, setting the sequence editor step to 12 should let you arrange your patterns with no breaks between them.
However, setting both rows per beat to 3 and pattern length to 3 beats as you've described will actually give you 9/8 (compound triple) time, which is sort of waltz-y, but might not be what you're looking for. Since most music cycles at 4 beats per measure, cycling at 3 beats gives the sense that the rhythm keeps folding over itself and doesn't quite resolve. Which is interesting, but again, perhaps not what you're looking for?
If you want more of a standard waltz in 3/4 time, you can set pattern length to 4 beats and rows per beat to 3 and still use the sequencer with step at 16. In this case, I think setting tpb to 6 should be unnecessary, since Pattern XP actually takes care of the tempo for you.