Its best to have the windows down, easier to remove. When reinstalling the new panels, put the windows up a few inches -new panels are very tight and can push against the chrome window frames making installation harder and making rolling up the windows very hard (everything is tight -until the windows are operated with the new panels.).
PUI panels for 61 to 64 chevy use repro top rails(wrong....-they won't stay on the doors.......) and they use individual nails in cardboard slots -nails done this way are cheap and break off and don't stay in place (ask me about a set of 1963 Chevy Impala PUI door panels it took me a week to salvage them...for a friends new 1963 Impala interior. Also the PUI 1963 Impala seats on his 63, had the wrong chrome buttons....
Paul