This has to be possible. I have an Apogee Element 24- I went an added two mono input busses.
A typical thing that I do a lot is create 2 audio tracks at once to record acoustic guitar. In every other DAW I’ve used when you do this, the DAW automatically assigns consecutive inputs to each track.
So hit the T key which brings up the create track window. I create 2 audio tracks, however I can only name one track even though I’ve told it to create 2 tracks; ok fair enough. Now when I name the track “Acky 1” it should create two audio tracks. Acky 1 with input 1 and Acky 2 with input 2. It names the second track Acky 2 but puts the input also at input 1. This is driving me CRAZY. It is a huge pain to have to stop and go into the track inspector and click on track 2 to change the input to track 2. Is there not a way to have this happen automatically like Pro Tools, Studio One and Logic? Is there a preference or anything"?
You could probably make a track preset with 2 tracks configured to your liking.
And then making new tracks from that track preset should create both tracks configured how you want them.
Actually no! it will still make the inputs input 1 even though I saved the preset with input 1 and 2
It’s very upsetting that this is the case- it’s crazy that you even have to have a work around for something this simple
Sorry - you’re right - looks like track presets don’t save save routing assignments (input or output). Looking at the manual, it seems that’s by design. 
You can assign consecutive inputs by selecting the tracks and holding shift while you select input for the first track. But this seems to only work if the channel configuration matches input configuration (mono track - mono input, stereo track - stereo input).
But in your case when having 2 tracks it probably won’t help much.