It's really hard. Evo-Web option file has near-perfect transfers, shirt numbers, flags and so on - which the JB patch certainly doesn't - and it has decent edits on the kits that haven't been properly done yet, so unless you only want to play the Premiership, you need to use it with the JB patch (the one with the edited kits -- then you go through the Premiership and the National sides selecting default kits for all of them, and taking off the edited sponsors, so at least the French and German clubs keep their proper kits). But West Brom, Palace and Norwich are a real problem. You can change their names, swap their kits back to default, and set ALL transfers to default - that magics those three clubs back into the game with their correct players. BUT setting transfers to default undoes the Evo-Web transfers and screws up the shirt numberings, so the teams are slightly out of date and a fair few squad numbers are wrong. But without doing that, you'll be there forever trying to work out where the Palace/Norwich/WBA players have gone, or who they've been edited into (remember, you can't go into Edit Mode and set them back to default, cos Edit Mode shows you the default rosters, before any transfers have happened, and those three teams all appear with their correct players in Edit Mode, but NOT in Register Player mode).
Best bet: just wait for a full kits patch, then you can use it with the Evo-Web option file for patched games (which sets all kits to default). Or, wait for an update to the JonBoyo patch and see what's in that.