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You will have problems if more than one copy of Calibre ever attempts to update its library and/or database as each copy will assume it has exclusive access and this can result in one copy of Calibre overwriting changes made by the other copy. This can occur if you make changes on one computer, and then leave Calibre running and switch to the other one to make changes.
Work is under way to rework the Calibre database layer to support multiple Calibre instances running against the same library safely, but there is no ETA for when this will be ready.
Having said that, it is OK for the Content Server to run in parallel with Calibre as the Content Server never tries to update anything. You can start the Content Server from the command line without loading the main Calibre program, and it sounds as if this is what you should be doing in your case.
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