Personally I stick to traditional instrumentation and haven't had a problem with it. The last few years have seen french horn players in the trumpet section (they do well!) and tubas learning trombone (I had a great section last year!). I've had clarinet players learn saxophone very successfully and you can have success with flute players there too. By getting your students to pick up the 'correct' instruments you generally make it to where you have some backup kids in your main band as well. Additionally UIL changing the rule for Non-Varsity concert bands means some of those kids may help your NV out in a pinch in the spring for UIL since they'd be on a different instrument. My JH and HS growing up both encouraged this doubling too and many of our students became better players for it!
Biggest thing is recruit a bass player ASAP. If you can't do that get a tuba player at least to play those parts - I had to do that my first year.
Personally my weakest thing probably is the warm-ups... I tend to just dive into the music. Spend time on 12 Bar Blues, blues scales, etc. When you're just getting started the Hal Leonard Easy Jazz, Easy Jazz Classics, and Swing Classics books are great for that. I'm personally not a fan of method books and prefer to teach from literature examples. YMMV
Biggest thing you're going to run into is finding a time you can get those kids together. In a 3A we share so many kids it is very difficult to get students to attend a rehearsal regularly. My first two years in my current district I tried multiple times to get something going and hit a wall when Basketball, Track, OAP, and Softball/Baseball started. I'm fortunate that my third year in the district we made it a class period that I've managed to maintain since then so we meet daily.
My e-mail is rashs AT oeisd.org if you have more specific questions I can help you with. I'm down in Odem just outside of Corpus Christi. Best wishes to you!
Odem High School