Why are you doing a 90 minute boil, exactly? What was the reasoning behind it?
I can think of only a few reasons to do a longer boil:
1. Using Pilsner malt (don't think that is the case here)
2. More hop utilization
3. To carmelize the wort more for flavor/lower attenuation purposes
If none of these fit what you are trying to do, then just use a 60 minute boil and save yourself 30 minutes on brew day.
If you still plan to go ahead, and the recipe is written for a 60 minute boil, then you should make adjustments to your pre-boil volume to compensate for the additional amount that will boil off during that 30 minutes.