The two tones make things a little tricky as most configs will give you an overlap of the tones in the middle position. That is, when in the middle with all three pickups on, both tone controls are 'on' (in the circuit) and having an effect.

Off the top of my head I can see three possible options:
1. Tone 1 for Neck-Middle, Tone 2 for Bridge-Middle. But, both tones would be active/on in the middle position (as above).

2. Tone 1 for Neck-Middle, Tone 2 for Bridge-Middle with no overlap. That is, the middle position with all three pickups on would have no tone control at all.

3. Change it to a single master Tone control, a master Volume control and use the other pot as a volume for the middle pickup. That would solve the Tone control overlap issue and allow you to roll off the middle volume and have just bridge, neck or bridge+neck like a Tele.

Thoughts?