We've been using MFL since it moved from FFLM a few years back. We run an auction league with contracts, Taxi, IR, signing bonuses, contract extensions on trades, and restricted free agents. It gets complicated, especially since you can never place a player on Taxi other than when you first draft or pick up from waivers (with a caveat or two). (The rule mechanics are surprisingly simple, but using draft software is a challenge.)
MFL is the only site I have found that lets me do what needs to be done, but it is still very kludgy on draft day. To do a draft using either of the commish-driven approaches, I would have to take several steps, on several screens after a bid was won:
-Add the player using the Load Roster screen
-Set the player's cap and contract length using the Set Player Salaries screen
-(Possibly) move the player to taxi (and bump someone else off) at Taxi Squad
This really slowed things down, especially in hour 10 of a 12-hour auction. It also got pretty risky, as it would not take much to screw up some data across all those screens. So, I got to where I would keep a round at a time offline (spreadsheet & paper) and then enter every round or so.
This year, I used the online auction capability, but not online. I used it just as commish. If commish has superuser on, you can set the auction to 1 player at a time and set the timer down to the lowest setting. I still conducted the draft live, but when a player was won, I was able to enter the team, player & salary in the live auction window and it was accepted almost immediately. I still had to go back in between rounds and add contract lengths, and I also had to do taxi manually, but overall it was the easiest draft I've ever had by far.
We did not use the software to track nominations. I was too concerned about the risk to use it for anything more than I did.