I'm guessing that you're referring to the tone control found in the MKIII/MKIV, since the MKII doesn't have one. If wired properly, it's bound to work in place of an output cap in any circuit.
For a simple thin/fat-switch just make C4 switchable. You could probably go as low as 2.2nF for a thin sound, but I would start off around 10nF. The downside of such an arrangement is that the fat position is going to be a whole lot louder than the thin position due to the fact that it has more frequency content.
A better and whole lot more flexible way of doing it is to utilize an output cap blend pot (which is basically what the MKIII tone control is) instead of a switch. Wire a 1n-10n cap between the collector of Q3 and lug 1 of the cap blend pot (100k should be fine), as well as an 18k resistor in series with a 100n between the collector of Q3 and lug 3 of the pot. The output then comes from lug 2 of the pot. This lets you pan between the small and the big output cap instead of a hard switch, and the 18k is a limiter resistor that attenuates the level of the bass side of the pot so that it matches the bright side. The 18k value is a mere starting point that I pulled from the MKIII and you will probably have to increase it in order to keep the volume uniform across the sweep.
The downside of such a blend pot arrangement is that it will suck some output level. I have no experience with the MKI but looking at the schematic, I would simply lower R10 until I got the volume needed. If I were to build one from scratch I would probably ditch both R9 and R10 and wire a 50k volume pot straight from the output cap blend pot to give an approximation of the original 100n/47k output filter, but that could end up making the pedal too loud.
