If you upload the UGC config files to your \tf\cfg folder on your server and execute the correct config file for the right map/gametype the whitelist and settings will all be correctly loaded.
To only update the whitelist file, make sure you download the newest on the UGC website and upload it as item_whitelist_ugc_HL.txt (or 4v4 or 6v6 instead of HL) in the same \tf\cfg folder as where the config files are stored. UGC configs will now use the new whitelist file when executed.
Executing the whitelist manually (with a custom one for instance) is possible by uploading the whitelist .txt file to the cfg folder and changing the loaded whitelist file with the following console command:
rcon mp_tournament_whitelist "cfg/whitelist_filename.txt"
rcon mp_tournament_restart
If your server is running TFTrue you can use whitelist.tf and enter the whitelist ID in TFTrue with 'tftrue_whitelist_id' to have a custom (or updated league) whitelist on your server.