Basically, you can just go by initiative. The line mechanic was only made to keep people to keep people from changing their target mid-combat to get some advantage. Going by initiative, like in most RPGs works just as well.
If you stack the units by who goes first, it might work out. IIRC, that is how many old map and counter wargames used to do it. Stuff that goes first is on top is on top of the stack.