Hi -
Obviously, you can't expect perfect behaviour from 5 yr olds, and having two makes it even more difficult! I can only suggest to make 'rules' as relaxed as possible, so they don't mind observing them, thereby reducing conflict to a minimum. Regarding waking and getting up in the morning, if that is a major problem, maybe have a rule that she HAS to wait until she is called to get up; I'm not a great fan of 'reward charts' but to have one for her staying in bed until called, marking each day she manages that, with some little treat for achieving a week without dramas, could help. Brother, of course, shouldn't be left out, so he can have a little treat too.
If you can have a consistent routine for 'after school', keeping them occupied or having healthy snacks or drinks, maybe a bit of TV, so they always know what is expected of them, and they don't get any unwelcome surprises. Also, I guess they need to do some reading, but if they are reluctant, don't 'push' it too much as it isn't vital at this age. Could they maybe do joint reading, so they take it in turns to read a page, or are they on very different levels, which might make that more difficult; though it might also spur-on the weaker reader.
I know it's not easy, but it's probably up to you to provide a schedule so the children always 'know where they stand'. Our DS used to sometimes be a bit 'lively' after school, but he would often have a little book and 'call the register' for mum and I, and then tell us what lesson we were going to do! (Both parents were at home through most of his primary years, which made it much easier.)