I'm not sure exactly what you mean by "I don't have to have the tuner on all the time". Do you mean you don't want the tuner engaged (tuning mode) all the time, or do you mean you don't want the tuner "on" (powered on) all the time ?
It sounds like you want to do option #1 which is just the traditional old school way as if you were going guitar to tuner to amp (or other effects pedals etc.). Makes sense, especially with your true bypass Turbo Tuner. When tuning, your guitar signal goes to the tuner and sound is muted. When not tuning your guitar signal goes straight through the true bypass tuner into the Helix guitar input. As with ANY true bypass setup keep your cables short like a 10 - 15 foot from guitar to tuner then short like a 1 or 2 foot into the Helix. Bottom line is keep total cable length under 20 feet.
There are reasons why someone might like option #2. For example if your tuner is NOT true bypass and has a bad buffer circuit that sucks tone you might not want to put that before the Helix. In that case you can employ the Helix external tuner feature (see Tuner section in the manual) to send your signal out one of the sends to the tuner that is always in tuning mode. That way your signal doesn't pass through the crappy tuner circuit while you're playing. It only goes there when you're tuning.
Another reason might be you want to bring the tuner closer to your face for visibility. I thought of doing that with a Boss TU-3S mini tuner (no footswitch). You could mount it to a mic stand to see it better but kick it in/out using the Helix tuner footswitch. Of course you could do that with any tuner - the TU3S is just small.
I was going to use option #2 with my regular Boss TU3 pedal tuner because even though it has a pretty good buffer I just thought it might be better not to have it before the Helix at all. I wanted to have my guitar going straight into the Helix guitar input. However I wound up going wireless with a Shure GLXD16 that has a tuner in it which is of course an active circuit before the Helix after all, but it sounds perfect and I prefer the tuner in the Shure over the Helix tuner. So I'm back to option #1 - just no guitar cable.
