I am not an electrician but have wired many remodels and new construction for myself.
Three way switches can be tricky...unless you do them routinely, having a good diagram is almost necessary.
First off...
You do have three way switchs, correct?
You need 4 way wire...one for ground, one for positive, one for neutral and one for "switch".
Depending on what you are switching, the s/u will change. I assume you are switching lights only.
This site has been helpful to me on this type of thing. Look at diagram #3 and #6.
Installing A 3-way Switch With Wiring Diagrams - The Home Improvement Web Directory