Building workspace means, whenever you make a change in the workspace -- saving changes to a file, creating a new file, deleting a file, etc., iTest will run a "builder" that checks for problems in that file and in any other files that depend on that file. To check for problems, the builder reads in the file and runs through a sequence of validations that are specific to the type of file. If a file changes, then iTest will also verify all files that depend on it.
iTest automatically knows about dependencies between files. If you're interested to know what those dependencies are, you can open the Dependencies view (Window > Show View > Other > iTest > Dependencies) and it will show you what files the currently selected file is dependent on, and what files depend on it.
If you import a new project from somewhere (e.g., from version control), then iTest needs to "build" all of the files in that project. Otherwise, iTest should only be building files when changes have been made, and only then to affected files. While the builder is running, if you want to see about what is getting built, you can open the Progress view (Window > Show View > Other > General > Progress).
Most files can be built extremely quickly. Response maps are the exception. To fully validate a response map, iTest performs mapping against all of the samples stored in that map to see if there are any new mapping errors. For very large maps, this can be time consuming.
Regardless of this, what you are seeing appears to indicate two unexpected things:
1) When a build happens, it always goes on in the background. So you should not be seeing that it stops anything else. You should be able to keep working without interruption while a build is underway.
2) Building shouldn't really be taking a long time to run, unless you have some huge new projects being imported or are saving really big response maps with huge samples.
Here are some guesses as to what might be happening: