Thanks for the latest replies. I think I may now have the problem cracked.
Having now browsed through the Calibre manual again, I see what AnotherCat means. I now know that Calibre users tags etc to create collections. I've looked at the PRS-T1 plugin in Calibre and found it is set to uses tags and series. As I had tagged some of the books as Amazon this would explain why an Amazon collection was created.
I've created a separate Calibre library ready for Mrs B's books. As it's solely for this purpose I will be able to create individual tags for each set of books downloaded. Anyway, as a test, I added a few books to this library and tagged some as 'Temp 1' and some as 'Temp 2'. I then got Calibre to send them to the PRS-T1 and, lo and behold, there were 2 new Collections, called 'Temp 1' and 'Temp 2' with the appropriate books in each.
And thank you for your link jackie_w. I shall study it carefully to see if there is anything else I can learn.
I am forever being surprised at the new things that I find that Calibre can do. Obviously the best software both before and since sliced bread!