Well this will of course in the end come down to personal preference. The way I do it is even though I am from the UK, I generally only import the USA games into Launchbox as they are generally 60fps Vs the 50fps of the pal roms, then I manually add any pal games that I am aware of that were not released in the USA, like Zero Wing on the Megadrive for example, which was JAP and EUR only.
I do keep all the other region roms in there respective folders just in case I hear of a great game that I don't have imported, so it's just a simple process of adding that single game to my Launchbox collection.