Goncalves was handed a shock recall for Sunday's 1-0 defeat at Dundee United, with the Jambos missing 14 players at Tannadice.
It was the Portuguese defender's first appearance under Jefferies, who had previously indicated the player would not be selected while he continued to refuse to sign a new deal.
"I'll have to wait to see who's available first before I decide who plays anywhere," said Jefferies.
"Today's the day we'll chat and set up how we want.
"Last week, I had a few players playing out of position, so there's one or two I'd like to get out of those positions and back into their normal positions."