The veteran striker returned to the Pompey starting line-up for the 4-0 loss at AFC Wimbledon, after a spell out with Achilles and calf injuries.
Whittingham was keen to ease back the former Republic of Ireland front man in a bid to avoid further complications.
But even though he has missed a month of action, Connolly remains Pompey’s leading goalscorer – with five goals to his name so far this season.
After picking up the injuries in the 4-2 loss at York in September, the 36-year-old was used sparingly as a substitute after making his return to action in the 3-2 win over Exeter earlier this month.
But with Patrick Agyemang set to be ruled out with a thigh problem for tomorrow’s home clash with Scunthorpe, the Blues boss suddenly has few options but to ask Connolly to lead the forward line again.
And Whittingham admits he is keeping a careful eye on how much he is asking of the striker.
‘If you ask David when he was fully fit to start a game, his answer would probably have been three weeks ago,’ said Whittingham.
‘We know we’ve got to involve him as much as we can because he’s such a good player.
‘But knowing that he has been out for a while, it does take longer to recover when you get that little bit older.
‘You’ve got to make sure he’s right and we can’t ask him to do too much too soon.
‘We need to look at the bigger picture because we need him, but we don’t want to risk losing him.’
It’s a tricky conundrum for the Pompey boss, especially as the bid to sign Jake Jervis continues to drag on.
Ricky Holmes is an option to play behind the main striker, Tom Craddock is just feeling his own way back to fitness, while Ryan Bird was knocked out in the defeat at Wimbledon and has not trained all week as he recovers.
Connolly, however, remains a key man in the Blues side and adds some much-needed quality when he plays.
Whittingham also knows he offers something totally different to the side, with his finishing prowess and his experience at the highest level.
‘He is a very intelligent footballer and he is very important to us,’ added Whittingham.
‘He works on the staff side as well as a coach, with some great opinions.
‘You look at him in training and see how sharp he is.
‘He’s a different player to what defenders are used to playing against in this league.
‘He’s clever, he takes up those good positions and is a finisher.’