RSRDC isn't really more "robust", just more "accurate", or in this case, since it's past history, "predictable". Lurker does have a better variety of ships than stock, and does have better looking "orders" for the submarines, along with having eliminated a lot of the stock game's "issues". Your surface ship, no matter which one you choose, nor the mod you add it to, will of necessity, replace an existing boat. ETR3(SS) has a "tutorial" of sorts on SubSim here, as does Peabody, and someone else also, but I can't seem to find them just yet. If there's no notes on how to do it in the ReadMe file of the ship mod, then download another mod and see if there's any instructions in it. Just remember that it'll be rather difficult to complete some of the missions, and impossible to complete others while in a surface ship. Some of those mods include Single (Quick) Mission files for you to experiment with. Those files can also be used to edit other MIS files, or create your own from in the Mission Editor. Each of the mods are a little bit different though, so we'd need to know exactly which of the mods you have to be able to help you more...
Another thing about using RSRDC, is that most of the surface ship mods are compatible with stock, so you have to do other tweaking to get them into RSRDC. Probably, when you install the mod on top of RSRDC, it overwrites parts of RSRDC that shouldn't be overwritten. Do the surface ship mod in stock first. Once you figure out how they do things in the Mission files, CareerStart.upc and Flotillas.upc files, then you can try to add something to RSRDC...