Hi @Steve_382 ,
Fairly straight forward and easy process to load and unload, but it just takes time. How much time will vary based on several things; How efficient you are at backing under the camper including making fine adjustments to get alignment and angle correct, if you use hand crank or electric drill adapter to crank the jacks, if you have another person to help (so you can both crank on opposite sides at the same time rather than you going around one jack at a time), how tall your truck is, the height you lower the camper down to after you pull out from underneath (onto a dolly or just for lower center of gravity), etc. Installing and removing the jacks takes some time, too.
The average person will probably have a bit over an hour into loading the camper (including jack installs) and a bit less than an hour removing the camper (including jack removals). Those times will likely be longer the first few times you do it, but as you practice some of the more time consuming parts will get faster (backing under) and you'll learn little tricks, like having the jack extended to the ground when you bolt it to, or unbolt it from, the camper so the jack supports itself rather than you holding it up as you start the first bolts and remove the last bolts).
Many owners do build a dolly to store their camper in a garage with a low garage door height. If you have a true 7' (if it's a 7' garage door, you may have an inch or two less than that depending on the design of your garage door), that is 84". The height of the camper from the footprint to the top of the air vents is 70" (A/C is taller). The jacks will lower the base down to about 10" - 11", but 12" is a save height to use and a good height for your dolly. So between the 12" dolly and 70" camper height, you'll be at 82" which should fit in your 84" garage door, but measure your garage door with it open to determine your true clearance. No need for using any foam/matt between the dolly and camper. That only increases height and since the dolly/camper will sit static (except for rolling it into the garage low speed), no need for a grippy/dampening mat.
I use a 5'x8' trailer to reposition our camper for storage in the off-season and then jack it up a bit, remove the trailer, the lower it to about 12" with a bit platform underneath (not a dolly on casters), but since you have garage door height restrictions, you'll probably not find a trailer with a low enough deck height to fit it through the garage door. Just use very large dolly casters and, if you have a nice smooth concrete driveway, you'll be good. Most use fixed casters on one end and swivel caster wheels on the other because using swivel casters on all 4 corners is hard to maneuver. You can use 4 swivel casters if your space requires it, but then you'll find it's easier to move with at least 2 people since they have mind of their own when positioning.
Presumably you'll load and unload immediately outside your garage door. If your concrete apron/driveway, in front of the garage door, is flat and on the same plane as the garage floor, all the better. If the driveway/apron is angled uphill or downhill, it will be more challenging the steeper the angle (keeping the dolly from rolling, jacking up and lowering the camper on a angled driveway, etc.)
There are no special connections to consider when pulling the camper off the truck and putting on a dolly. Your dolly should have crossbeams and flat plywood surface for the camper footprint to rest on. The camper base is perfectly flat. The pins, that interface with the front mounting brackets in the pickup, are on the sides as are the water drain hoses and DC wires/connector. The dolly surface need only be approximately the same size as the footprint (57" x 82"). A dolly surface an inch or two larger or smaller than the camper footprint is inconsequential, but making it very close to the same size is more satisfying. Ha. And, just make sure that the width of the dolly, or trailer, fits between the jacks.
There is no issue having the camper brackets, truck wiring, and camper installed on the standard pickup bed now and moving it to the Bowen tray later. The only consequence is a bit more expense (or time if you are doing it yourself) associated with moving the brackets from your pickup bed to the tray and also moving the DC wire connector from the pickup bed to the tray. I might suggest that you let STC know you may move the camper to a Bowen tray later, with which they are very familiar, so they can potentially account for that when they install the DC wire. Consider having them NOT drill the DC connector hole in the bed of your pickup and rather zip tie that connector. If this will be temporary, and you sell/give away the pickup bed, no reason to have a hole drilled in the rear of the bed for the next owner. And STC should know about how much extra wire length, if any, they need to give you if the Bowen connector mount is in a different location than stock pickup bed. If you temp-mount that connector and later decide you are not going to get a tray and instead keep the pickup bed, you can always have the connector permanently mounted later.
Regarding the Bowen bed, if you decide to go that route, just make sure you are getting the version for a slide-in camper, rather than the true flatbed tray. A flatbed tray is at least 3" taller than standard pickup bed and so you may have a larger gap between the pickup cab roof and the bottom of the camper cabover. Not sure what pickup brand you are putting it on, and that is less of a problem with certain pickups. For example, Ford Superduty have such a tall cab that STC puts a 2" foam mat under the camper so it clears the Superduty cab. But Bowen knows all the specs for various pickup make/models. The slide-in version of their tray keeps the main part of the tray about the same as stock pickup bed and then the wheel wells stick up a bit into the side boxes. It's not a flatbed tray, but a specific tray build for slide-in campers.
That's all I can think of off the top of my head. Just ask if I didn't cover anything or some of the above triggers more questions.