I think your plan for handling skill rolls and what-not is just fine, and it shouldn't be hard to get your players to go along with it once they know what's expected.
The main thing I've learned from about 25 years (holy crap! I must be nearly dead!) of GMing is that by and large, players prefer fair to kind. As long as they know that the GM isn't either gunning for them or coddling them, most people will accept the times when nothing seems to go right. I know that when I'm playing, if I know the GM is always going to fudge to stop the worst from happening it takes a lot of the fun out of it for me.
In a similar vein, don't play favourites. Never, never, never. That includes NPCs -- if an NPC you've lovingly created somehow doesn't work out, or is stabbed through the liver by one of the players in a fit of pique, just file off the serial numbers and use it somewhere else. If your Significant Other is about to fall to his or her death in a pool of boiling lava, DON'T fudge it if it's going to be in any way obvious to the rest of the party. I'm not saying that you can never fudge a roll, but it should always be for a purpose. I tend to do it when a character would be killed through no fault of their own in some non-heroic fashion, but even then I tend to leave them with some kind of scar to remind them not to go skinny-dipping in otyugh filth next time.
There's lots of other advice you can get, but I really think that being scrupulously fair with the players is paramount.