There are several potential solutions to this common problem.
1. Get a sub which already contains all the necessary controls. Pass through, variable filters, phase inversion etc.
Costs a bit more but it's a one stop solution. You might even get a remote control.
2. Get a pro multichannel audio interface (DAC). Use separate channels for mains and sub.
Use the included software to filter, phase invert, EQ etc etc. Good basis for expansion.
3. Get a monitor controller. With more than one output pair.
There are specific 2.1 controllers but a simple one will do.
4. You could also use the booth out, mono sum or sends found on many mixers. There is also a whole class of devices called distribution amps.
Probably too many channels for home use and the good ones are dear and the cheap ones cheap.
5. If money is a real problem you could probably get away with a splitter cable and one or two inexpensive volume controls.
Bit of a kludge but will tide you over.
In your position I'd suggest you have a look at this NI Audio 2.
It's inexpensive @ ~$100. Send the same output to both output pairs and use the handy individual gain controls for mains and sub.
Could also act as a dual headphone amp for late at night. Free copy of Traktor into the bargain.
N.B The examples linked are simply devices I am familiar with. You can get similar products from many manufacturers and spend much more or even less.
Edited by RonaldDumsfeld - 9/10/13 at 8:21am