Not sure if this is any use to you, but what's I've done is to use multiple numbers in the series index. That is, the first box set with books 1, 2, 3 would be 1.23 while books 4, 5, 6 would be 4.56. This works until you get more than 9 books in a series which, for me, has happened once. At that point, I just changed the series to whatever box and used the standard 1, 2, 3, 4 numbering.
You could create a custom field but too much of a pain getting it to the series field on my ereader.
There is an older thread on this topic. You can find it at
Enabling entry of multiple books of same series for Boxed Sets.