If you are talking about the two long bolts that hold the thermostat housing to the intake manifold then be VERY careful!!! Clean the threads of the bolts with a brush and then put some never seez on the threads. Reason I say this is because I went to go change my thermostat one day and one of my bolts was a bitch to turn ... Finally, it broke right at the top of the threads. Bottom line, intake manifold had to come off, had to drill the bolt out (ez outs didn't work), then had to re-thread the hole! PITA!
So if you put never seez on the bolt threads, you shouldn't have issues with removing the bolts ever.
If these are the bolts you are talking about, for my 98 GT the recommended torque is 15-22 lb-ft.