So as written we can't do what you've said, but I'm missing some detail.
Our custom draft order tool mostly lets you do whatever you want, with one caveat: when the dust clears, every team has to have the same number of picks, any of which may or may not be pre-populated with players. If you make a team give up two picks to keep one player, something has to give; if your league really does expect them to start the year down a player, then yeah, we can't help you. But if you just mean you want to shuffle the draft around so that they get that last guy at the end of the draft, we can do that. It is a pain, but it sounds like with the system you have in your league it will always be a pain for the commish to set up a custom draft order no matter what/where you do it.