SH, the 2600 can do a fine job with auto-calibration, but a little user input can make it even better. The auto process tends to set speakers where they're capable of operating, but this might not necessarily be the very best setting. In particular, it's a good idea to have speakers set "small" and with a 80Hz crossover even if they have good response to lower frequencies; instead let the sub handle what it does best and take part of the load off of the speakers and the receiver amps. Study your manual and you'll notice that in the auto-setup menu you can set it to "skip" some of the measurements. Skip the speaker "size" measurement and instead manually set all speakers "small" with an 80Hz crossover, as the manual specifically suggests for THX speakers.
Also, don't be concerned if the distance measurement for the sub would come out longer than the actual physical distance. A delay in the sub amp's processing could cause its sound to arrive as if the sub was actually farther away. Some users have misinterpreted this as an error, but it's actually more accurate(trust your 2600, not your tape measure).
Enjoy the music, not the equipment.