I'm no professional pilot (...yet) but I do travel quite a bit. I have basically a drag along stewardess-style (if you don't mince too much nobody notices..!) overhead-compatible bag, with a zip up compartment in which you can put a smallish briefcase-style laptop bag (that comes with it). If you need extra space you can put a coat in there or something, check the bag and carry on the laptop bag bit of it (which is usually what I do), and it works fine with the laptop bag sitting on top with the handle through the extended handle of the main bag.
Sounds complicated but works very well. However having had it for 5 years the zips (it all relies on zips) are getting knackered. Made by a company called Solo, don't know if they're still making them.