Toilet bolts must have been part of the drain pipe and hub originally installed .Bolts rusted off new bolts came with the toilet but won't slide in the slot

Can u give us a picture. The channel for for bolts has a square cut out at one end. This is so bolts can fit in and slide to position.

Are u sure the bolts supplied with toilet are the right bolts?

Chuck

The original bolts were not part of the old FLANGE but they could be rusted away, usually they are brass and do not rust. Your flange should have two slightly arcing slots which are open at one end. You drop your johnny bolts into the slot and give it a 1/4 twist. How to Install a Toilet: How to Replace Toilets and Weather Stripping | eHow.com