This is something that first got me when i started playing the game.Very frustrating in the beginning.After some game time i got the hang of it.i was using line for most of my moves,it just didn't work for me.For Assaults i switched to using an arrowhead and for a defensive move a vee.Much Better.I think the footprint is just a rough estimate.To get them to fit in you'll need to micro the companies.Give your HQ a Defend order with in-situ then micro each Company and put them where you want them,then simply re-attach to your HQ and they'll stay put.If forced to retreat though,they won't try to retake their former positions
This something i asked about before,i think the footprint modifaction is on the list for the new engine when it comes out.