If, as I'm assuming, they're 12v 'lead-acid' (i.e. car / leisure / gel / agm) batteries then yes, they should be fully re-charged for storage, the top wiped clean of any residue and stored in a cool dry place if possible. they would benefit from a brief top-up charge periodically - over winter I'd say 3-4 months is okay between top-ups but if stored at room temp then maybe 1-2 months between top-ups.
In use they ought to be re-charged before they go flat - I try to recharge mine before they drop below 12.0v; if you let them get down to 9v they won't last as long; <9v and you'll be replacing them very soon.
Not sure what they mean about a normal charger not working - a modern 'intelligent' charger may not work if the battery is flat as they need something typically >9v to detect that the battery is there and connected the right way before they turn on. Unless the batteries are sealed types - i.e. gel or AGM which ought to be charged with a charger that has a 'gel' setting. Were they supplied with a specific charger?