Table view with custom cells

You're going to have to maintain a list yourself to determine which cells should be checked or not. Remember that in tableView:cellForRowAtIndexPath:, a proper implementation will recycle cells so that you never have more than 10-15 cells instantiated. This can cause some funky results if you don't handle for it properly. When I've done a poor implementation, I've seen certain cell properties "carry over" from one cell to the next.

Anyway, here's what I'd recommend (based on what I think you're asking):
1. Create a class to back each UITableViewCell
2. Create a property in that class to determine which of the two checkboxes (or neither or both) should be checked.
3. In your ViewController/TableViewController, maintain an NSMutableArray/NSArray where 1 item in the array = 1 cell in the UITableView.
4. In your tableView:cellForRowAtIndexPath: method, get a reference to the appropriate item in your array.
5. Then, check that instance's properties and set the checkbox values appropriately.

TableView.h

@interface TableView : UITableViewController 

@property (strong, nonatomic) NSMutableArray *itemArray;

@end

TableView.m

@implementation TableView

@synthesize itemArray;

- (UITableViewCell *)tableView:(UITableView *)tableView cellForRowAtIndexPath:(NSIndexPath *)indexPath
{
    // Assume you get a valid, custom UITableViewCell at this point (named "cell")

    // Configure the cell...
    NSObject *classItem = [[self itemArray] objectAtIndex:[indexPath row]];
    [[cell checkBox1] setChecked:[classItem checkbox1Checked]];
    [[cell checkBox2] setChecked:[classItem checkbox2Checked]];

    return cell;
}

@end

Well you should not use the TableView as the datasource.

Every time the cell comes into view the UITableViewDataSource is asked for the UITableViewCell at as indexpath.

- (void) tableView:(UITableView *)tableView setImage:(UIImage *)image forCellAtIndexPath:(NSIndexPath *)indexPath 

In the is method you should set the checkbox state as it is reflected in your dataSource. When the checkbox is changed save it in the data source with the selected state.

Example:

- (UITableViewCell *) tableView:(UITableView *)tableView cellForRowAtIndexPath:(NSIndexPath *)indexPath {
    static NSString *cellIdentifier = @"CheckedTableViewCell";

    CheckedTableViewCell *cell = (CheckedTableViewCell *)[tableView dequeueReusableCellWithIdentifier:cellIdentifier];

    if (!cell) {
        [[NSBundle mainBundle] loadNibNamed:cellIdentifier owner:self options:nil];
        cell = (CheckedTableViewCell *)self.nibCell;
        self.nibCell = nil;
    }

    item *item = [self objectAtIndexPath:indexPath];

    cell.titleLabel.text = item.title;
    cell.switch.on = item.selected;

    return cell;
}

You could save the state in NSUserDefaults right when you click it. Just add a target with @selector(changedOne: ) and add the void statement:

- (void)changedOne: (id)sender  {
    NSUserDefaults *df = [NSUserDefaults standardUserDefaults];
    NSString *row = [NSString initWithFormat:@"toggleOneRow%i",indexPath.row];
    if (sender.on) {
        [df setBool:YES forKey:row];
    }
    else {
        [df setBool:NO forKey:row];
    }
}

Are you using cellForRowAtIndexPath. If yes, then instead of

 static NSString CellIdentifier=@"CellIdentifier"

use

 NSString *CellIdentifier=[NSString stringWithFormat=@"CellIdentifier%d",indexPath.row];

Other approach you can take is assign tags to checkboxbuttons and take one dictionary in appDelegate file and set value for checkbox tag.initially you may set is either checked or unchecked.and set the values in cellforrowatindexpath method. set the values of checkboxes as per appdelegate dictionary.and update the state in appdelegate dictionary when user selects or deselects the button.