In the audio preferences area if you click 'Drivers' you should be able to pick what inputs get recorded.

PT will take the one that is highlited and closest to the top and make it the assigned track once the recording is 'kept' using keep take. The rest will autamatically be assigned to the next available track. There isn't much you can do about that at this point except move the track to where you want it afterwards.

It has never really been a problem for me, as it is possible to rearrange the track order in the tracks window.

The thing to pay attention to is whether you are recording a mono track. If you want them in stereo pairs, change the track to Audio-Stereo. If you want monos, use mono, and make sure the 'Mono input' selection box (again in the audio preferences area) is assigned to Left, Right, or Both. This selects whether to use L&R or just the left, etc.

You'll want 'both' in most instances so you can either have input 1&2 be recorded as a stereo recording (using that track format for the target track) or treated as separate mono tracks (by selecting mono as the track type before recording)

Hope that wasn't too confusing. The combination allows recording however you want it, and there is always the 'split track' or 'merge two mono to stereo track' function available if you want to change them.

I do not work here, but the benefits are still awesome
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