this brochure might be useful for info... Check your manuals supplied with your trailer for your axle/brakes and see if they have similar info.
I like to raise the wheels just under the flat area where the shocks mount too. I also agree you should safe up the side you are working on with frame jacks but I would be hesitant of using the frame jack to lift the whole trailer off the ground. Use the axle jack to get the wheel off the ground then use the frame jacks for some lifting to make the side stable. I also like the idea of leaving the truck connected to the trailer to keep it from rolling on you.
You can also roll the trailer dual tandom wheel up on a higher ramp type stand that will lift the other wheel axle off the ground that will allow you to rotate that wheel to make adjustments... Eats up alot of time getting things just right but is pretty safe...
Jacking up the frame persay has its hazards. Thats alot of stress at that one point on the trailer frame. You certainly don't want to warp the frame. Jacking at the axles to lift the frame is no different than going the road stress wise. Then safe up the frame with jacks to make it stable - not lifting the whole weight... I guess it doesn't really matter what you do first but I would just jack the frame to remove some weight and then do the axle jack game plan to get the wheels off the ground.
I have jacked up my single axle OFF-ROAD trailer several times using this method of jacking the axle and only have adjusted the fifth wheel 28-foot trailer brakes one time doing this same thing.
After doing the fifth wheel that one time I think I will take it to the dealer and let them do it the next time... They have a hugh pull through garage all setup just for this... I notice you never see any RV trailers in PEPBOYs or other car/truck tire places... No problem with my 4200lb OFF-ROAD POPUP trailer.
These photos from google search look pretty safe to me..
just my thoughts