If you haven't already found out 'the hard way', copying a 3TB drive with a lot of data on it to another 3TB drive is quite time consuming. And double that if they are external USB drives!
My methodology is I do everything on my SSD drive. Each shoot is in a clearly named folder in My Documents, and in that folder is separate folders for RAW, JPG SOOC, Selected JPGs, From LR, From PS, and Cropped. I also copy that entire folder 'as is' after completing each nights' worth of processing to my internal HD. That way I always have a backup, and every 'stage' of processing is backed up as well. When I'm finally done with a shoot (I don't do paid anything), I'll copy the specific catalog name from the Lightroom folder into the 'shoot' folder, and then copy the whole thing to the HD, then remove all of it from the SSD.
I have a duplicate HD, and both HDs are in slide in/out bays. So I slide in the 'backup' HD and copy just that shoot folder from the 'regular' HD to the backup HD using Windows methods...no special software. If I were to copy the entire partition using special backup software, it would take over an hour. And that's with both drives internal 6gb/sec SATA 3 with a 4.8ghz quad processor. I also copy the folder to my external USB backup drive, and then return it to my off-site location. Overall, I'd call this a do-it-yourself 'incremental' backup (backing up only that which has changed, not 'everything').
To my way of thinking, one of the advantages of my methodology is I always have at least one backup for everything (I've not mentioned the USB thumb drive version of the shoot in my pants pocket until the off-site copy is off-site once again) and that if needed, I can fully recover everything for a shoot without having the LR index 'bogged down' with lots and lots of shoots/pictures/etc. If I do have to go back to LR, I simply put the folder back on the SSD, and copy the LR folder back to its' spot as well, and go to it. But then, I don't use the LR catalog for any purpose other than in-process editing. My very specific folder names, and folders within folders within folders to identify a specific shoot and multiple folders within each shoot are enough for me. Should I want to find a specific shoot, no problem. Finding a specific person in multiple shoots, that's why my 'final' shots are JPGs, and viewing the folder as icons helps me find who I am looking for.
So, given your setup, I'd keep the shoot on USB drive #1, and, having both drives plugged in simultaneously, copy the shoot to USB drive #2. Just be VERY CAREFUL about what drive letter is #1 and what is #2. Having the internal drive names different is very helpful. Alternatively, there are various backup software products available - and even in Windows, IIRC, that can do 'incremental' backups...copying only that which has changed or is new.