First let me make sure I understand this correctly.
You have some of your SIL's family in a separate family file and YOUR family file. You want to merge both files into one, and exclude the duplicates. Is that right?
If so, you'll want to Import the separate SIL file into the YOUR family file. Then you'll want to merge the duplicates.
Either way, you need to know how to Import. Before you do anything at all, backup both files and in this instance, I'd back up media files too.... just in case.
The first way (more cluttered, but fewer steps):
Open YOUR family file.
Click File > Import > Legacy Family File
Select "Have Legacy create a list" (or you can navigate if you wish, this will be certain though)
Legacy will search for that file type and then select the SIL file.
Select the second option, the current family file.
Go ahead and let it do a backup, another won't hurt.
Now, look at these options carefully. Choose the ones that you want/need. I recommend the following settings:
Records to Import: All; Show combine options: checked; Record Numbering: try to keep; Valid temple names: checked (if you have LDS, else unchecked); Format names: your choice; To-Dos: checked; Exclude LDS: unchecked (unless you have a reason otherwise)
Click AutoSource. Now here again, this is per preference. There are valid reasons to select either one. I personally like sourcing each detail I ever find. This way I know where I got it. However, you're only importing and it's likely you just want a note that says "this file was imported from xxx" and in this case, I think that's sufficient. Whatever, just choose which ones you want and create a Master Source however you wish. Mine is usually Imported from XXX file and I always keep that original file.
Now it's going to go through and tell you issues and combinations and whatever. Read it carefully if you get any. Some examples are one location (like New York City) has Longitude and Latitude and in the other file that same location (New York City), doesn't. They're usually minor, but go through them one by one as they come up.
It'll finish, say it's complete and then ask if you want to go to Merge now. Say yes.
It'll prompt for another backup, so do that.
On the Normal Duplicate tab, pick your options. Personally, I'd check off everything on the left side and everything under Take into Account.
Now on the Special Duplicate tab, you may have your own ID numbers on the individuals or whatever. Choose whichever matters most to you, if any of it does.
Now hit Continue
Overwrite? is a personal thing. I don't recommend overwriting any of it. If there is a mistake or it's a mess, you can always go back, delete this file and merge again after you see the issues, so I strongly recommend not only keeping the earlier backup, but checking off Always keep earlier backup so you never make the mistake of overwriting it.
Now it goes to merging.
Keep in mind that it will merge the right person into the left one, which is odd. I always think of left to right but whatever. They don't. Let's say LEFT Joe has a different birthday than RIGHT Joe.
If you're not sure about something, then click Skip to Next. You can ALWAYS look for duplicates later and do it again. In fact, you can skip this step entirely if you wish and do it later.
When it's done, you're done!
It sounds overwhelming and time consuming and depending on how many you have, it can take a lot of time, but it's really not all that hard. The hardest part is the merging and making sure you're merging the right person. Given your description, it'll probably do well in merging and not be that difficult.
I probably need to make a video on how to do it. I have to learn how to do the video thing, but I probably can learn that fairly easily. I'll try to set that as a goal by this weekend, if possible.
You might try reading the Help file, in particular Importing Files into Legacy. In Legacy click Help > Help Index > Click the Index Tab then scroll down to Import then Files into Legacy.
Good luck and I hope this helps you.