A manual x-fer switch with it's own sub-panel feeding just the circuits you deem critical could be added, and wouldn't interfere with the whole house transfer switch at all.
If all these circuits are 120v, you're portable units should work fine, up to their capacity, and would easily protect a couple refrigerators/freezers, and run enough lights and other small appliances to get by.
I'd strongly advise you to seek the advice of a qualified electrician, as it will have to be wired correctly to ensure everything works safely.
Unless you need power for medical equipment though, you may find that the cost of the needed equipment and labor may be more than it's worth, vs. a good maintenance and test regime on your existing generator to make sure it's always ready to run.
Yes sir, I do not perform electrical work of this nature; I might install a simple wall switch or receptacle, but I hire professionals for this level of work. My questions are simply for my understanding, not for DIY activities.
All of the intended circuits would be 120v. I perform all of the maintenance on the existing unit with assiduous detail; you really could eat from it. New oil and filter (with magnet attached to filter) annually even though it only has about 28 hours on it and it is just now approaching 4 years old. I adjusted the valves per specification at the 24-25 hour mark, and I also increased the monthly exercise time to 25 minutes because I was seeing some "oil pudding" on the fill cap. That has stopped since increasing the exercise time.
This potential project is just an attempt to bridge a potential issue:
The problem that I have is that there are zero Generac authorized servicing dealers anywhere near us; plenty of sales and installation dealers, but no service dealers, and none who are willing to come from any distance. (I discovered that anomaly AFTER purchasing the ten year extended warranty. In my own naivete and ignorance, I did not imagine that a dealership that sells and installs units would not service them.) I contacted Generac and they said words to the effect that in the event of a unit failure, they would "find" a way to provide service. That did not leave me with a overwhelming feeling of confidence that during such a failure event that the process would be easy and convenient.