Hi Justin,
There are probably as many opinions on breeding as there are breeds. That said, it depends on what your purpose is. If for instance you are breeding Delawares, which I am, I'm not as concerned w/ show quality as I am in purity. So I have my roo and hens together continually. I also have marans. For those I select only the darkest eggs to hatch.
As for leaving the roo and hen together, I understand that it takes two weeks for her to get the old roo out of her system. So you can go from there.
I suggest doing some research. I know we'd all like someone else to do it for us but I haven't found an easier way. The public library is an excellent place to start. I took out every book I could get and then some of them twice. "Back Yard Poultry" magazine is also an excellent magazine as is "Practical Poultry" from the UK. Subscibing to BYP is cheaper than buying individual issues and since some issues carry over to the next month. The $ 15-20 a year is worth it. PP is very expensive at 7.50 an issue but worth it for the information and perhaps can be shared w/ a friend or friends to cut cost.
For those not familiar w/ PP here's a run down of this months issue. "Hybrid Vs. Pure Breed" , "Alternative Sebrights", and the reason I bought it, Poultry Keeper's A-Z. Covers all kind of chicken related issues for the letter E. Each month is a different letter.
The part I liked is "embryonic positions" covers the different positions of chicks in the egg and why they fail to hatch. "Epistasis" covers genetics. Specifically the term dicscribing the inhibiting action of one gene over another.
What I learned is that the white leghorn always breeds white but it carries the genes for barring and colour. Interesting huh?
So Justin, I'll stop here. It really isn't possible to tell everything there is to breeding on this post and even if I could you'd miss the exciting things you'll learn along the way while doing your research.
All the best to you
Rancher