If they're Speed Daddy headers, it's worth to replace the one they come with anyway because they tend to leak after a while.
If the shop knows what they're doing, they should be able to cut out the old flex and weld in a new one that you provide, it's an easy job.
And just my 2¢, if I were you I'd have the shop weld in that new flex and whatever else you want them to do, and then install it myself. You'll save a bunch of money on labor, and there's a good writeup on here by BillBoost that makes the job doable for anyone with basic hand tools, maybe a swivel or two.
