The former Motherwell, Aberdeen and Bristol Rovers boss was asked to become Gordon Strachan's assistant when his former Dons team mate was appointed as Scotland team boss last month.
Their first game in charge is against Estonia in a friendly at Pittodrie on Wednesday night and McGhee accepts that he now has to take a different attitude to such fixtures.
He said: "Like every club manager you take a selfish position but Gordon and the team we have here have been as sympathetic as we can and doing as much as we can to accommodate clubs.
"Clubs are the first port of call and we will give them as much respect to gain as much co-operation as we can.
"But I think there is a little bit of a conflict and now we are on this side, it is gamekeeper turned poacher."
Strachan immediately faces a club versus country issue with regards the four Celtic players in his squad; Scott Brown, Charlie Mulgrew, Kris Commons and James Forrest.
The Hoops are due to play Juventus in the first-leg of their Champions League last-16 clash at Parkhead on February 12 and with that in mind, Neil Lennon has spoken to Strachan, his former boss at Celtic.
McGhee, though, insists Scotland's new manager has not decided how much game-time, if any, the Hoops players will get at Pittodrie.
"There has been no decision about that yet," he said.
"There is a very good understanding between Gordon and Neil but even before I was officially appointed I had a text from Garry Parker (Celtic coach) with reference to that game.
"I can't remember exactly what he said but it was something like 'you do know we are playing Juventus?' sort of thing.
"But I think we will respect that and respect how important a game it is for Celtic and we will do what's right."
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