First in a certain line, second cutting in — bother! (6)
I believe the answer is:
pester
'bother' is the definition.
(I know this)
'first in a certain line second cutting' is the wordplay.
'first in a certain line' becomes 'Peter' (Peter I was the first pope).
'second' becomes 's' (common abbreviation).
'cutting' is an insertion indicator (some letters cut their way into a word).
'peter' placed around 's' is 'PESTER'.
'in' is the link.
(Other definitions for pester that I've seen before include "Keep bothering" , "Be a nuisance, annoy with requests" , "Bug" , "Annoy with frequent questions" , "Nag, badger" .)