You could keep a NSMutableArray* called checkmarks that stores NSNumber instances. 
Set +numberWithBool: on each element of checkmarks as YES, for example, to mark all rows as checked.
Note that this is just a data model store. Thus, you have to actually read the values of checkmarks in your -tableView:cellForRowAtIndexPath: method to set the checkmark states for each row's accessoryType, e.g.:
cell.accessoryType = ([[checkmarks objectAtIndex:indexPath.row] boolValue] == YES) ? UITableViewCellAccessoryCheckmark : UITableViewCellAccessoryNone;
When you programmatically change the state of checkmarks, you can then call [tableView reloadData] so that the state of table view rows reflects the state of elements of checkmarks.