First, when you create the .inc with the Repackager Wizard, you'll be prompted for data like company name, etc. - and the name of a template (in .ism format) if you wish to use one. There is a default template, identified in my earlier reply. You can use Developer to modify it, or you can create/specify your own.
If you have a list of additional servers which you would like to have in all of the packages you create, I would suggest adding them to the template that you plan to use when creating the INC. This way, you create the list once (in the template), then apply the template during the repackaging process.
If you have one package that is an exception to the template, you can either edit the MSI package in Developer or create a transform to use with the MSI package on distribution.