Working Mechanisms

My suggestion would be to find out why they're not working, first.  If it's an electrical/pickup problem, then they may be able to be wired together to overcome it.  If it's a mechanical issue, you'll need to sort that out or you'll just end up with a 0-6-6-0 that doesn't run.

Speed

You will also need to see if they are the same mechanism and are speed matched.  0-6-0's usually have small drivers so it would be a pretty small engine.  For a Mallet, the front cylinders should be larger than the rear cylinders, so you might need to build up the size of the cylinders.

Next you will need to figure out how to work out the suspension.  Normally a real articulated has the rear engine rigidly attached to the boiler.  The front engine is hinged to the rear and slides side to side under the boiler.  A lot of model engines have both engines hinged and linked through the boiler.  You will have to find a boiler that has enough space under the front to allow the mechanism for the front engine to fit in it and swing to accommodate the front engine turning.

Definitely doable, but

Definitely doable, but probably quite a challenge.  By the time you get done, you will practically have scratchbuilt the mechanism - so in that case it may be easier to just start from scratch. 

Depending on the manufacturer of the 0-6-0s, you could probably use the frames, side rods, valve gear, and cylinders.  The front cylinders would at least need to be modified to remove the cylinder saddle (where it attaches to the boiler).  The frames would need some kind of hinge to attach them together.  A boiler could be fashioned from the two 0-6-0 boilers by cutting and splicing to make it longer.  Other piping and details would then be added. 

The mechanism would be tricky.  You could get two NWSL gearboxes and modify the 0-6-0 frames to accept them.  Connect the two gearboxes with universal couplings, and find and mount a suitable motor.  If you were thinking of a "two motor" version using the existing mechanisms - I see some major issues here.  The front engine needs to pivot below the boiler.  Unless this is a saddle tank 0-6-6-0, the boiler won't be wide enough to allow the pivot with a motor in place. 

Some Possible Ideas

There was a really good article years ago in Model Railroading magazine that might offer you some suggestions. You can probably find it on the TrainLife magazine index. What they did there was build an early articulated similar to B&O's Old Maude, an 0-6-6-0 that was America's first Mallet. They used the mechanism from Mantua's articulated logger and the boiler from a Tyco Chattanooga Choo Choo. I don't recall the tender but they ended up with a pretty nice 2-6-6-0 similar to D&SL prototype. Perhaps there's some ideas that might help you along.

Barry P.