Isolation transformer and scope when troubleshooting SMPS
Power the circuit you are testing thru the isolation transformer, and the scope normally (not thru the isolation transformer).  It does matter which of the scope or circuit you isolate, since the scope has a chassis and connectors that you can easily touch.  You want that stuff grounded so that the dangerous parts are a little harder to touch.

Note however that as soon as you connect the scope ground to some part of the device, all the other parts are now at ground-reference voltages, meaning they are no longer floating.  You can get seriously zapped if you touch one of those other parts and ground at the same time.