Only have that problem when a few on each side are engaged with each other. In those instances we just pick them up change the dial/slider and put them back down in roughly the same spot. Its not been an issue.

I found in my few games that if one didn't want to remove the squadrons from the board, I'd just have my opponent hold down his desired squadron in place, so I didn't swat it around with the movement tool. (also found curling the tool in odd ways helps too).

Otherwise, I think one only need note which squads are engaged, and since they can't disengage until they're done fighting the movement/position of them was ultimately irrelevant. It could make a difference once the fighting is done, but I've found nothing substantial. Actually, I think that when fighters are engaged for a few rounds slight movement on them is thematic, indicating that they are 'flying around' in that particular space.

Hell I might even try some house rules that make the squadrons flip place each round. changing their board position entirely depending on how long they've been fighting.