From the sounds of it, you should separate to begin with and read a bit more into breeding before thinking of pairing them together again. Also, why are you breeding? Just for babies? Might want to take a more in depth look into reasons to breed vs reasons not to.
As far as your questions...
Leaving the male in? You'll get mixed responses. Some people say separate because of the chance of breedback (male impregnating the female right away). Some people say it's fine, breedback isn't common, but if you DO find you have a male that breedbacks, separate him every time. Like I said, in your situation, I'd separate and take some time to look more into breeding basic FAQs and reasons to/not to. The male will be fine you separate them.
Signs of labor - If you're lucky, you may see contractions. Or you may not. I've been in with the chinchillas one night to my female acting normal, the next morning there are kits in the cage. Many people are the same way. You usually only see signs of labor if there is an issue because the female has been in labor for so long, she can't pass the kits, or like I said.. if you're lucky.
Bedding - Most people handle kits fairly soon after birth to get weights, check sexes, etc. Moms do a pretty good job of cleaning up after themselves after giving birth, so you don't have to clean too much up. She'll hang out in one spot of the cage to birth, so you may only need to clean out that corner if she doesn't.
Read through the FAQs of this section, that will answer a lot of basic questions about breeding.