Yes, get them onto straight comb! It can be a sticky and messy job and unfortunately some bees may not survive.
Move the hive a couple of metres away whilst you mess about with it, in this way the flying bees will return to the old site and not bother you. I would also suggest having a queen cage (or matchbox) with you, so if you find the queen, pop her in for safety. (Easy to say, not so easy to do if you are not familiar, but you can pick her up by the wings using thumb and forefinger or guide her into the cage with a finger or hive tool).
One thing you might like to consider is to use a second brood box if you find the queen. Place this over a queen excluder and over the brood box with the messy comb, place drawn comb and foundation above the excluder and put the queen in there. (If you have some brood for the top box that would be much better). Then feed the colony to encourage comb to be drawn and after 3 weeks, the bottom brood box and the wild comb can be removed.
The photo is of a 'cut-out' where a colony was recovered from somewhere unsuitable and the brood comb was fixed in an empty frame. You can see the masking tape being chewed through after a week or so. Later on the bees made good the gaps and filled the frame.
Welcome to the forum btw.