If you have both Hopper3 receivers setup to see each other then you can select which Hopper3 the Joey is linked to. You would select “Whole Home” under Dish diagnostics. Under detected devices you would see both Hopper3 receivers and you select which Hopper3 you want to link. However, you mentioned that you wanted the two Hopper3 receivers to be isolated from each other. In that case your 4 Joey receivers will only see the Hopper3 that they are connected to.
If this is a matter of privacy, not wanting anyone else to see the contents of your DVR and its recordings, then if you want it to be impossible for others to see or access your Hopper 3, then you MUST have Dish/tech install an isolator. The tech should have some in his truck and there should be no extra charge, but tell him BEFORE he does the install work. The Isolator prevents two Hoppers of any kind from seeing each other, most often used for matters of privacy like the parents don't want the kids to see any of the "Adult content" mom and dad use to spice up the marriage .
However, if your concern is that your parents might somehow mess up your Hopper 3, then I would NOT have an isolator installed because the Joeys are PAIRED to a particular--ONE--DVR only and, it is impossible for them to mess with your timers, or otherwise access any of your settings, etc. Further, the process to see the other H3 and view the content requires additional steps that most people just have no clue how to do. No guests I've had who have even stayed multiple weeks have no clue there is another DVR to "see" nor how to achieve this. All they look at is the recordings that show in the DVR screen and watch Live TV. That's all they care to do.
In my case, I've nothing to hide from dear old mom (yeah, I'm that boring!), but I wanted our Hopper 3's to have the ability to see each other because sometimes there are shows dear old mom has recorded that I find out later, I want to see, and I have occasional recordings that either she wants to see our we watch together. Also, if I am in the Living Room where mom's H3 is located and I doing things in the Living Room, I have watched MY H3 recordings through her H3, and I don't want to lose that ability. Those points of flexibility are important to me, as well as being able to PAIR any of my Joeys to HER H3 if MY H3 DVR dies and has to be replaced, so I don't miss my shows, in the RMA meantime . And NO, dear old mom has NO CLUE how to access the other (my) H3 even if she were offered a million dollars. You'll find most people don't know how to access the other Hopper. The kids can figure it out, but parents of a certain age? NEVER!
Tell us how it all goes with the install, and if you want/get an Isolator installed.