Is there any way to have the parts of an Alternate be displayed in a report. I can only get the description and the cost but no parts.

The software is designed to only include original, "base bid" items in the proposals with the idea that "alternates" embody changes to the base bid, or items that arise after the contract has been signed.

There are two ways to get around this, however:

1) Open the alternate, switch it to a "component", and then click "Save". Now, the parts included in the alternate will be added to the main estimate and therefore appear in the project specifications.
-or-
2) Open the alternate and then duplicate it as its own project for the same customer. You can now load this project and print it off with full project specifications by itself, or sub-totaled along with the main project.

Here are some links you may find helpful:
To duplicate a project: http://www.clearestimates.com/online-manual/204.htm
To change an alternate to a component: http://www.clearestimates.com/online-manual/212.htm
To incorporate multiple projects into a report: http://www.clearestimates.com/online-manual/224.htm