A few Flying J locations do have free overnight parking for RVs. You can download a Flying J RV guide from their website which lists the facilities each one has.
And as mentioned, there are no hookups, so it is "boondocking" only.
There are two guides though - so I am not sure which one is the most accurate. The webpage below has a .pdf, while the top drop down menu of the Flying J website allows you to download a spreadsheet. I am not sure if there is a difference between the two versions or not.
Pilot Flying J
The ones that say "Yes" to "RV Parking" are the ones that offer overnight parking. Other amenities that some Flying J's have are dump stations and RV-only fuel lines.
Last spring we took a trip in our car to Florida and back with our car. We went to visit our son (lives in Florida) and took a cruise. Anyway, we had just bought our RV so we looked for such places. So we reconnoitered a route for a future RV trip when we drove to Florida from Michigan.
We found several Camping World locations that had free overnight parking, but they only had a few spots. One place, near Pooler, GA only had electrical hookups, but only 4 spots and they were already occupied at noon.
If you go to the Camping World website and look up the various store locations, it will tell you if there is free overnighting or not.
We only stopped at one Flying J; near Ft. Pierce, to look it over; and it looked pretty nice.
We also looked at other alternatives; such as reversing our schedule (drive at night and sleep in the day) and sleep at rest stops (which should be a lot safer in the daytime). But some states have restrictions on how long you can park there - even in the day time. North Carolina I think has a 2 hour restriction.
Of course there is WalMart where you can stay (generally called Wallydocking - a synonym for boondocking), but what we found is there are plenty of RV parks right off the highway, so the safest and easiest method for us is going to be to stay at those places; especially if you are a discount club member, such as Passport America, etc.
Other locations, such as St. John's County in Florida have a county-wide ordinance on wallydocking.