Mike.. the parts are not fixed length.

Your first select is returning great results but the occasional '~' is on the end of some records.

B005739997706~

I added a replace on the SecondString.

select substring(docid,charindex('~',docid)+1,7)FirstString,

replace(substring(docid,CharIndex('~', docid, charindex('~',docid)+1 + 1) + 1, 7),'~','') SecondString

from mytable