I wanted to use FlashBuilder and FlexBuilder on the same system. I felt the documentation for this flow was a little light, so here's a summary of my findings & the issues I worked through.
First attempt: Use the same Workspace in both FlashBuilder and FlexBuilder
I wanted a smooth migration, so I tried to go slowly. I wanted to be able to switch between FlashBuilder and FlexBuilder while working on a shared project in a particular Workspace. The dev environment requires Subversion, Maven, and particular folder locations identified in uniquely named environment variables (I'm using Windows 7). It is not feasible to duplicate the dev environment since it would require lots of overhead management of files, update, etc.
FlashBuilder installed without disrupting FlexBuilder. I opened it and pointed it at the Workspace. FlashBuilder's Problems panel lit up with red. I worked through the issues, but some of them involved compiler settings. Changing those settings messed FlexBuilder up, and that's the tech we agreed on for this project. I reset the project files by using our Maven script and moved on. I wasn't going to be able to use FlashBuilder & FlexBuilder interchangeably in this Workspace.
Second approach: New Workspace, import Preferences
I nuked FlashBuilder's Workspace history so I wouldn't accidentally bork up my production code projects again. I had some custom display settings for my FlexBuilder editors and I really wanted to use those in FlashBuilder. It's fairly time consuming to set all text editors to have black backgrounds with light-colored text that 'plays well' with line highlighting & custom colors on reserved words, etc.
I used FlexBuilder's 'export preferences' workflow & saved the preferences to My Documents. I then used FlashBuilder's 'import preferences' workflow & restarted when prompted. One of the preferences, apparently, includes Workspaces. I was promptly shunted back into the Workspace I just 'rescued' and borked it up once again. Fixed it the same way as before & moved on.
Third approach: New Workspace, Flex 3 Compatibility
It was clear I couldn't work on my production code in both FlashBuilder and FlexBuilder. I still wanted to play with Spark and incorporate it into my music player project.
I created a new Workspace for FlashBuilder, closed FlashBuilder & ensured the Workspace history only included that Workspace. I then restarted FlashBuilder and manually changed all my settings to the stuff I mentioned above. I quit & restarted to ensure I wouldn't lose those settings if Eclipse froze while I was mucking about.
I opened my music player project & saw the familiar red warnings. Internet searches weren't very helpful, so I poked around. The first thing I did was go to my root mxml file and type "<Spark" and hit enter to force the namespace into the root of the project. I then right-clicked the project folder & chose 'Properties'. I had already set the SDK to 4.0 under the 'Flex Compiler' tab here. Under that selection area is a checkbox that says "Use Flex 3 compatibility mode". That's the key. The Problem panel degraded the errors to deprecation warnings and I was able to run my music player in debug mode.