Best advice I can give you is to only use options 1 & 2, and the transfer funds allocation tool on the trainer. Don't use the super budget one - as most clubs have good funds prior to you taking over.
Once you've used options 1 & 2, save the game. Once you've done that, go to your boardroom, and look at the wage slider. Edit your budget so that you have the slider to the wage budget side, and you'll increase your wage budget exponentially.
Realistically, you can play the game without using option 3. Only thing a really bad budget will do is not allow you to increase your staff pool whilst the budget is in the red.
I'm using Man Utd, and I'm doing fine, but I'd love to increase my Physio allocations due to the high injury rate that team seems to suffer, but I can't increase it over 6, because the club is in the red. I didn't use the cheat to get me there though, it was just that Man Utd has very top heavy finances. Not at the stage where I'm getting "club is going to die" messages like I was getting before when using the cheat.
Its probably only a minor glitch in an otherwise excellent trainer, and it doesn't seem to be a problem that affects everyone.