I use all three modules. However, there are limitations depending on your question. What are you looking to do?

Hi.

Is there a way to populate job cost with all the line items (which are data base items) into an estimate?  When we import an estimate into job cost, no data is transferred except the estimate number and the project name.

What about estimated budget total? Cost Codes? Extras ( sub Jobs?)? 

Are you using project management as well? Not saying you need to but, we had an issue with our data getting hung up in there. 

Also, are you tracking your job status in Sage from Un-started to In progress to Close?

Are you running an inquiry to check your data or report?  New or Current status?

No cost codes or anything other than the estimate number and the project name is transferred.

Yes,  we use project management,  track job status, etc.

Our problem is that currently we have to enter (re-type) an entire contract line by line into job cost. Is there is a way to transfer all that data from the estimate automatically.

Yeah, that is exactly what happened to us too. We got rid of Project Management. Our data was very all over the place. 

We stopped using it and things have gotten alot cleaner. 

However, so you are aware, when you use PJ, you are going to want to run your reports and inquires out of PJ. That is the only way I was able to get some visibility when we had issues.