Do it on the head, It's easy. Compressed air holds the valve up, the engine holds the head in place. You compress the springs, pull the locks and reverse.
Installed height for the two springs will be the same, it's set by the valve length and retainer / lock combo. If you can reinstall the valve spring without compressing it a bit, then you have an issue and should stop immediately. Most likley, you will need to compress the valve spring, and you will have some force on it (that is your seat pressure)
While you are there, just for your piece of mind, measure the fully compressed spring and compare it to the installed height.
installed height - compressed height - .050 = max valve lift.