I know it's late to the game - but after reading - here is what I have been doing. I have my Helix paired with an AudioBox as an aggregate device - so I can access all the inputs at once. - now I have inputs 1-10. When I record into Logic - I select the track I want for the channel - no 1/2 or 3/4 but the single Helix channel I want (Helix is 3-10 in the aggregate - AudioBox is 1-2)
Basically - on the Helix - you need to click the output block at the end and tell it where to send the signal. If you're getting them in the DAW as 1/2, 3/4, etc...then use them as they are grouped - eg. guitar to 1/2, vocals to 3/4...otherwise if they are single channels (1,2,3,4,etc...) just send each to their own channel. Then in the DAW you need to select that input for each appropriate channel.
It's not as hard as it sounds and actually becomes second nature after a little while - just pay attention to what is going where.