Hi Tommy,
"Numbers are issued by the ministry" just means that you'll automatically be supplied with the next sequential numbers. So, if yours is a new flock number, they'll automatically start your individual animal numbers at 1 and increment upwards from there.
As long as you still have any unused extra tags in your possession, ordering too many isn't an issue. When you use a tag you need to record that in your flock book, for instance "10 lambs tagged, UK0{flock number}/00001 to 00010".
I just checked the registration letter they sent us with our flock number on it, and yes, they did only quote six digits eg 123456. The number that goes on the tags is therefore UK0123456/{sequential animal number issued by ministry}.
Does that answer your questions ok?
Edit: P.S. The Shearwell SET tags are really good and don't get lost often. The one disadvantage we've found with them is that you can't read the number at a distance. As a result, we now use a "SET" tag as the EID tag and a "combi mini" as the visual tag, which is still small enough not to be a problem, but big enough that I can read the number from a couple of sheep-lengths away. YMMV though, depending on how often you need to know their numbers.