I've done it more times than I care for... probably more than 5 times in various leagues & sports. Also, since they are auctions, it is even more complicated.
What I ended up doing was saying that the team(s) I would draft for had to provide a list, and I would draft exclusivley off that list, and always bid the max amount, and never go higher. So if (for example) Alex Rodriguez was on his list at $40, and someone bid $1 for A-Rod, I would immidiatly bid $40 for that guy, and that would be the end of it. Then, as teams finished up their drafting (or used up their money so they couldn't participate) I would pass the responsability over to them.
Generally that would incent the owners to show up for the draft since they would know they would be over-paying for players or they'd be left with the people chosen at the end (which might be sleepers, but unlikely). In compensation for that, I would give them first rights to the waiver wire (a 1 day head start). It works alright, but it is very bad since as commish, I not only have to draft my own team, run the auction, track everyone's cap space, but also draft for one or more teams (most I ever did was 4, but that was a very small draft where they only needed one or two players a piece with very little money available).