You have control over that in your fleet control MFD. That is the one that brings up the formation choices. Choose your formation and by repeatedly clicking that formation you can choose which position you will occupy. Your wingmen will move to fill the other positions. I don't think you can control which vessel takes which of the other open spots.
After that you can choose tight, medium or loose formation. This is very misleading as what it really does is order your wingmen to either fire at any target, fire only at your target or hold fire until ordered or manually triggered. If your pop up description is on you will get a brief description of the other controls in the display when you hover on the control. Tractor, capture, defend, use overloads, use stealth... etc. I have had the controls not respond to input on occasion but it only seems to get locked out at the start of the mission. When the next skirmish launches the controls usually work again.
One thing you can do that I only discovered recently is plotting a coarse. From the bridge of the starship you can shift + click on the waypoint you want and do so for a sequence of them. A diamond thingy appears on the point you clicked on and the starship will steer directly for it. This is true also if you set up a sequence of them. It will navigate to each one in sequence. This can be done for each vessel but you must transfer over to each ship in order to execute this.