If you don't care about true bypass of each effect when the other one is used, you could use a special DPDT on-on-on switch on the output of each effect. These switches are a bit hard to find, in the center position they connect the center lug of each pole to the opposite lug.
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/ | \ left center right
[o=o o] [o=o o] [o o=o] -> Fx A output Fx B input input jack/Fx A input
[o=o o] [o o=o] [o o=o] -> Fx B input output jack Fx B output
Fx A both Fx B
And then use traditionnal bypassing for the whole box.
If you do want individual true-bypass, the simple and effective way is to use standard bypass for each effect (as if they where in two separate boxes) and two footswitches. Keep them close enough to stomp on both at the same time, and you can do all the combinations : bypass, fx A, fx B, both.
That's what i did for a TubeDriver and a Phase 45 in the same box, and it works like a charm, with two Millenium bypasses.
You could even put an FX loop on the link between the two effects, have a look at the "Proco Juggernaut" thread.