Barr Britvic Soft Drinks will have its registered and legal headquarters in Cumbernauld, North Lanarkshire, but its operational base will be in Hemel Hempstead, North London, where Britvic has been located since March.
Roger White, AG Barr's chief executive, who will run the combined company, said it was "rather simplistic" to say that the important decisions will be taken down south.
He said: "Who will work where, if you like, we haven't made any comments on yet because that is still subject to being fully reviewed."
Mr White has told investors he can strip £40 million of annual running costs from the new company with plans to axe between 8% and 12% of the workforce. Some 500 of the existing 4300 posts are likely to go.
If cuts fall proportionately, it would
see 120 roles go at AG Barr, which employs 980 people.
AG Barr has operations in Forfar in Angus and Pitcox in East Lothian, as well as bases in England and Wales. However, Mr White said no decisions had been made about where the cuts will land.
The uncertainty over jobs comes as unemployment rose in Scotland by 4000 between July and September but dropped across the UK as a whole. It is the second successive quarterly rise north of the Border.
Headline unemployment now stands at 218,000.
At Westminster, MPs demanded answers for the Cumbernauld workforce in light of the merger. Labour's Gregg McClymont, MP for Cumbernauld, Kilsyth and Kirkintilloch, who is seeking an urgent meeting with Mr White, said: "I'm seeking clarity from Britvic about whether the staff levels at the company HQ will increase or decrease as a result of the merger."
Margaret Curran, the Shadow Scottish Secretary, said: "AG Barr is one of the town's biggest employers and the workforce will want reassurance about the future."