They'll fit.
When the rails aren't bolted to the floor (like when the seats are our of the car) if you use the seat adjuster lever, the seat rail will close in on itself, just like it would when you slide your seat back/forward in the car, the difference being that in the car, one section of the rail remains stationary, allowing the seat to move forward/back.
With the rails not bolted to the ground, both parts of the rail will move, the result being what you're experiencing now, the bolt holes not lining up to the chassis holes.
The fix is simple, turn the seat on its side/back so that you can see the rail. From there, you'll need to adjust the rail until they're in the same spot on both sides (count the holes on the rail and make sure the 'teeth' are in the same holes on either side). Once you've done that, put the seats back into the car, and you should find the holes will line up just as your stock seats did.
If you used the seat lever on your stock seats with them out of the car, then tried to re-fit them, they'd look like they weren't going to fit either until you fixed them as above.
Hopefully that made sense...Of course if the rails have been changed from the standard, the above won't apply.