Seems that I now am passed the configuration issue. Selecting to create a deployment manifest, and then using that on the server, allowed me to specify where settings where supposed to be read from, as well as supplying the server settings. Next problem is that apparently we have not got the oledb engine for automating excel installed on servers, so now I have to battle the operations team to get that sorted :P.
Should anyone else be in need of a smiliar solution, this is what I did:
1. Created a xml-configuration with the values I wanted (I choose one config file for each SSIS package).
Tip: If the file does not exist, it is created by the wizard, so all you have to provide in the name of it, and path will be set to your SSIS project folder!
2. Activated the option Create deployment utility, which is in the projet property page under Deployment Utility.
Tip: do not keep this active during development, it can build and increment your manifests and when it has done so 4 or 5 times, it starts to get bugged... (information from a more experienced colleague)
3. Built the project
4. Copied manifest, dtsx files and dependencies (config and excel files in my case) to the server
5. Double-clicked the manifest to run it, followed the guide to install and configure my packages.
Tip: If you have more than one configuration file, pay attention to the drop-down box where the name of the configuration file is displayed - you need to choose each file you want to configure! (I almost misstook this for a regular text field and thought next config file would appear as I stepped to next step in the wizard).
Voilá! All done!