Need tips on how to Crate train a 3 yr old Female... with boys that mark everywhere?!

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Ok,
this is my situation. Monica has been with us since 12/09/09 She is a darling little thing. She is not trained to go outside and goes on the pee pad about 1/2 the time. Other times she pees in the middle of the floor.
She does not do this often so I am thinking of Crate training her. I feel terrible though. I really think she could get the hang of it. Well my question is this. I have 2 males in the house that wear wee pads because they like to mark and sometimes a little pee comes out.
How can I train her and then she might smell their pee somewhere and get confused and try to pee there instead? I want to be able to take her outside and teach her to use the pee pad as well.
I saw a good youtube video on how to get them used to the crate without all the crying and barking. The thing is not to make the crate seem like a punishment.I tried a few things I saw on the video and Monica went in the crate to get her treat , each time I put the treat further and further in the crate and she went all the way in. I know this can be frustrating but I really feel that she is very worth me trying! Any other tips on how long she should stay in there??? Here is the video I saw.

YouTube - How to Train Puppies : How to Crate...

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