Not to start a flame war and with all due respect the only basic difference between a starting battery and a deep cycle battery is the thickness of the plates and the distance between them.
It's true that starting batteries will not get you very far and will likely go bad in a short period of time from deeply discharging them but they will still work.
The OP has stated that he already bought them so the only advice we can really give him is that the next time he needs batteries, get all 6 and make them deep cycle.
As far as the charger overcharging or blowing up starting batteries has no merit. Although the charge rate is slightly different, if any battery can take a higher and faster charge it is the starting battery, deep cycle batteries prefer to have a slower charge.
The full charge shut down for most ferro resonant chargers is around 2.54v per cell which equates to about 45.7 v for a 36v charger. As a side note, an automotive alternator generates about 2.5v per cell.