>I'm using Inventor 2008, and the project files do say read only
which part says read only (the project file, or the style library or other)?
You will want to make sure the Project Location points to a top-level directory and all the parts are stored in this directory or directories nested in the top level. Also, you will want to make sure that your parts are not in any folders which are contained the in the Libraries portion of the Project.
Which view of the BOM are you looking at (there should be three tabs). If you are in the Parts Only tab, and you have parts in a Normal assembly, you will not be able to edit the parts. Instead, switch to Model Data tab, and drill down into the assembly. There you should be able to edit the parts.
>To be honest I'm a little foggy on the difference or why there is a boms, and a part list separate.
A BOM is essentially global and it contains everything in the assembly. A Parts List is a view of the BOM, specifically for a drawing. This seperates data from formatting.