To be honest I have done this both ways. I have had my HD650s directly into the headphone amp of the Emu in the front, and through the same port w/SR71, and finally the output in the back w/ the SR71. The back is the best, no doubt about it. But changing the rechargeable batteries in my amp is getting to be a major nuisance. I'm used to akalines that go for like 50 hours, but the rechargeables only do around 5 hours. It is during the recharging that I run the headphones without the SR71. But there have been a few times where I got lazy and left them there for a few extra hours.
Recently I found another alkaline set I never used, so I'm giving the rechargeables a break, and now they are connected the correct way to the mini-line out in the rear. I have the "Main Output" knob maxed for this configuration. Sounds terrific.
But to make a long story short, use the back if you have an amp. Also make sure NOT to use the back without an amp, as I imagine that could ruin your headphones, due to too strong a current.