If it were me I would probably build them individually in series, into a combo pedal. (see more on combo builds on the Guides Page)
Each with its own bypass switch and volume control for the most tonal variations.
Then additionally you can use the Tone TwEQ by itself without the Pony engaged so you can alter tonal effects to any other pedals in your pedal chain which would be the most versatile move of all. This would be similar to how people would use an EQD Tone Job pedal except you would put 2 circuits into a single combo pedal to save space, or obviously, you can build them in their own enclosures.
Anything else is just chopping away at your options. IMHO.