You've left out a lot of details, but I'm thinking write up thier lease like this: $650 for one person in one bedroom or $800-$850 for two people in one bedroom. You have to charge more per person, otherwise soon you'll have 3, 4, 5 people living there. Everyone will want to be a freeloader. But, since the additional person isn't taking up a whole new room, the second person shouldn't be the same price as the first person.
You don't want to charge so much more that you lose both. But, you don't want to charge too little since it will be a headache for you and you will have additional utility expenses. What would it cost them if they move out and get a place of their own? If they can get a place of their own for ~$900, I can't see any reason that they'd pay you more than $800. But if they can only get a place of their own if they pay $1000+, then they will gladly pay you $850.
Don't write it up in a way that her rent drops. For example, don't give them both $400/month rents. Why? Because then he'll move out and she now only pays you $400 instead of $650. Also, don't write him a lease for $200, since then she'll move out and you only get $200 instead of $650. You have to have it done in a way like I said above, $650 for one and $800-$850 for two.
I'd keep the utilities included. I see no reason to change that part of her deal. You know for a fact that they are being paid on time every month. Finally, you don't have to do the math and beg them for their part every month.