No they don't. I hooked up a 640a and sat/sub system for my next door neighbor. I've also hooked up a similar setup at my house, in a couple cases trying a mono sub output from the Outlaw RR2150 receiver and another time using the line level sub output from an Outlaw 950 pre/pro. I've also used an Amber preamp/power amp combo without a sub output, and had to use the speaker level outputs to the Mirage subwoofer. In my case, the Amber stack with speaker level inputs had the most satisfying sound and was easiest to attain good tonal balance.
If the 640A doesn't have a sub output, the 540 definitely doesn't. I say use the speaker cable inputs and enjoy the music.
You'll get your best sound hooking the satellites and the subwoofer directly to the speaker outputs on the amp. Running the satellites full range may reduce ultimate dynamic range, but it does wonders for continuity and especially soundstage.