I think there'll be more overlap than you think. Your Perl 5 knowledge will serve you well when you pick up Perl 6. I think knowing more Perl 5 will make the transition easier, not harder.
For instance, the syntax of hash refs may change from $h->{foo} to $h.{foo} (I think ;-) but not the fundamental notions behind hash refs. Similarly, becoming better at Perl 5 OO programming should directly improve your Perl 6 OO programming. The fundamental concepts won't change, only the details.
That said, it's also true that some areas will change more than others. If you haven't picked up formats, for instance, you may want to wait until the appropriate apocalypse. XSUB programming is another area whose changes are unclear. But overall, I'd recommend to dive right in, and plan for the transition only when you feel the need.