Marc,

First of all, your problem is not unique as there are other users asking the similar questions. In fact, we are working 
on a new feature in the next release of Momentics IDE to ease the source check-out and project creation side of the 
problem. You are welcome to comment in this wiki page on the feature

http://community.qnx.com/sf/wiki/do/viewPage/projects.ide/wiki/F27IntegrationDesignDoc

Now go back to your specific questions:

1) How can I do this automatically? (checking our source)

You can use the Eclipse Team Project Settings File (PSF). You can create a reference workspace, check out the correct 
source tree (BSP, ResMgr, App) and create build-able projects from the source checkout. Then you select your project, 
export them as a Team Project Set file. You share your PSF file with your team so they can simply "import" from this PSF
 and get the right source tree check-out.

2) And how do you share the header files and make sure they are found?

Same as the above steps. Header files are either in your "stage" directory - where you have Momentics SDP installed, or 
for your own header files you can create a reference project holding header files and setup the project dependency. You 
then check-in the reference project and include it in your PSF.

3) Automatically package several IFS images and other files into one firmware package?

I am not sure if this can be done without an automated build setup. This is a question on the product release and it 
almost requires a formal build. But for your experimental works you can use Eclipse ANT script and create a launch 
configuration to run the ANT packaging script after your build your projects. You might be able to automate your full 
project build using ANT too.

Hope this helps,
Andy