If you have only one install of Silent Hunter 4, no problem. With the Fall of the Rising Sun Ultimate mod enabled, you then build your mission with the Mission Editor as you want it to be. Each mission you build has to be built with the mod that it will be played in, enabled, in order for the ME (Mission Editor) to make the proper "Calls" to the game's "assets" (ship, planes, subs, etc.). With Single (aka: Quick) Missions, you have to have a player submarine added to the mission, and set to Human Control, which is a little "tick" box by the Docked Ship tick box in a Unit or Group properties box. Your mission date, and the submarine entry date should be the same. Most other vessels, it usually doesn't matter, but it is also a good idea to have them all set to appear at the same time and date also. If you gotten all of that set correctly, the really BIG thing to do is that when you "Save" the file, you save it with a name, in a folder with that same name, in the SingleMissions folder.
In other words, you have a mission that you are going to name "Sink The Nagato". So you click on the "File" menu, then "Save", and you get a dialog box to open. Type in your mission name, which in our example is Sink The Nagato. Now "highlight" the text (hold down the <Shift> key, and press the <Home> key). Press the <Ctrl> key, and while holding it, press the letter <C> key. That will copy the text of your mission name to the Windows clipboard. Now use your mouse, and navigate to the Data / SingleMissions folder in your game folder. Once you're in that folder, and see all of the other folders there, click on the New Folder icon up in the top border of that same dialog box, which is the folder icon with what looks like an asterisk on its corner. It will than make you a folder that is highlighted, with "New Folder" highlighted also. If you then press the <Ctrl> key, and while holding it, press the letter <V> key, you will paste the name of your mission into the New Folder name text location. Press the <Enter> key to complete that, then again to open the folder. Now press the "Save" button in the bottom right of that dialog box, and you have your file saved in a folder of the same exact name. In theory, it should show up on the menu in the game now.
What some folks forget to do sometimes, is to use the menu item "Mission" and then "Language Localization", and type in a MissionTitle. That's when you'll see "mission title" on the game's menu under Single Missions. Just select the MissionTitle text in that Language Localization window, and type your mission title in place of what's there. Press the OK button, and the window closes. The only other thing that you should mess with in that dialog would be the MissionBriefing section, where you can type in text that describes the parameters of your mission, and what is expected of the skipper.
There is a Mission Editor pdf file somewhere that I cannot find just now. If I can, I'll post back with a link. In the meantime, to get you started:
SH4 Mission Editor Tips
SHIII/SH4 mission editor
There are quite a few postings on this site with ME info, so just use a search engine, and see what you can find. The ME Manual that I was referring to above, is actually an SH3 Manual, but it is almost the same Mission Editor in both games, with just some slight display differences, such as that Mission menu item (all of those used to be on one dialog window), and in the ability to save both US missions (using the "MIS" file extension, and German missions (using the MISGE file extension).
If you still have issues, don't hesitate to ask.