Question about breeding

The female kept running from the male and started to bite back is that normal should I seperate or no?

Not that I've vastly experianced, but I would seperate. She's indicating that she's not in the mood. Keeping them together is just risking stress and a possible fight. Is she ovulating?

well she laid her first clutch last week

So they've been together for a long time then. Are there any other geckos in there with them? If you're going to do a permanent colony, you should have several females to one male...this way the male can focus on breeding other females for awhile. When you have a one to one ratio, the male constantly will pester the one female leading to a lot of stress. In that case, they should be separated. Usually breeding visits are for only a few days, that's all it takes for the season normally (they retain the sperm).

i know this I only put them together once I wanted to reintroduce them. How long should I keep them together? 3 days? 2 days? a week?

That someone else may need to answer. I would separate as soon as you see problems. I was going for 3 days with two of my girls and took both out after two days. One because I could see several bites on the female, the other because I could see a bite on the male. If, for some reason the breeding didn't take, I'll reintroduce after she's laid 2 clutches of duds. My girls are first year breeders, so I'm 1/2 expecting the first clutch to be bad. If your girl laid good eggs on the clutch she had, there's no need to reintroduce them.