best way to connect two subwoofers

How do you plan to locate them?

Mine are hooked up right channel to two subs and the left channel to two other subs.

1 on each outside side of the focal about a foot behind the speaker itself

Do it the easy way.  I just saw the specs on the subs, very nice set up capabilities, but configuration is still manual. 

Solve your integration issues first, and separately.  My guess is that once you do you'll be so happy you won't care about other options.

Of course, subs work better with great room treatment.  If that's on your agenda, do it first, then sub configuration.

The first set up method you mention is correct.