Well each pickup is sort of suited more for each position in terms of the magnets, output, EQ balance, etc. So if you put the neck in the bridge and vice versa, it will sound a bit different. Basically, a neck pickup is designed to be 'warmer' or 'more smooth' whereas the bridge is more for clarity and lead playing but a lot of that is due to the output/balance. Each pickup position also has varying outputs based off how high/low it sits in the cavity and along with these other factors I mentioned. In the end, you want to play in the pickup position to create the sound and tone that you need/want for whatever music you are playing.

So really you can put each pickup in a different position but just be aware that for EQ purposes it might no really 'make sense' to put what would be a neck pickup in the bridge and vice versa but it really will come down to your wants.

Also with an EQ pedal you can impact a lot of the tone no matter what pickups you use. I'm surprised you can't get a good 'heavy tone' out of a Tele, I find them much better than a Strat typically is for heavier tones unless you're going for some ultra high gain metal or something.

On a side note, I would personally swap to the DiMarzio Chopper T + Twang set, IMO its a great way to get a humbucker distortion with a nice clean single coil in the neck. Its up to you but for EQ purposes I wouldn't want a humbucker in the middle.

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