On the Fleet Boat side, you would be editing files in the "Data / UPCData / UPCCampaignData /" folder - on the German side, it's "Data / UPCDataGE / UPCCampaignData /":
1. "CareerStart.upc", if you add-in career start locations.
2. "Flotillas.upc", for the dates of the active flotillas, and the outline of assigned missions
3. "PatrolObjectives.cfg", which hold the information for the missions assigned in Flotillas
If you study the Stock files, and compare them to say TMO, you'll see some changes. Compare those to RSRDC, and you'll see even more.
All three of the files work together, and a simple mistake in any one of the three can wreak havoc, so always work from copies of the files, and build your changes into a JSGME mod, so that you can more easily back-out of an issue.
If you're mostly doing the German side in SH4, try Operation Monsun, since lurker did what you describe in it... This is the same issue that keltos01, Peabody, myself and others have been trying to overcome for the Japanese submarines in Climb Mount Niitaka. Their boats went all over the place and change home ports like I change socks. Ya know? At least once a month...
