Katheryn,
If I were you, I'd weigh my options. You said that your SIL is coming to your house (I’m assuming using her own gas and vehicle), is very affordable and helpful. It also sounds as if this is not a daily routine, so even if it is an annoyance, it is not something that you have to deal with all the time.
Yes, you are correct, out of common curtsey, she should have asked. I am guessing that she just assumed that it would be ok, some people are like this.
It is probably easier for her to have 2 six year olds, because they play together, and probably help out with your daughter too. Unless this child becomes unruly and monopolizes the time your SIL should be spending watching your daughter, I would not worry about this.
As for the other things, eating in the back of her car, marker, etc, everyone has a different parenting style. Is this really something to worry over? Is this worth ending not only affordable child care, but creating a rift in the family? I would mention these things once, and if it is the worse thing that annoys you, consider yourself lucky and let it go. If it becomes an issue of safety (not wearing seat belt, etc) that would be the time to sit down and have a talk.
Call a couple of child care centers and ask their rates. I think that you will find that for the price, your SIL is well worth the money (and the slight aggravation).
Buy your SIL a thank you card; tell her how much you appreciate the services. My guess is that she will be so touched, that even if you do bring up some of the things that are bugging you, it might go down a bit easier.
Hope this helps,
S.