I can see endless problems dragging this out for some time for the OP, so maybe it would be best to suggest this now rather than waiting.
If you're trying to use a flash drive as if it's a floppy drive for booting a computer, you may be lucky and have a co-operative BIOS that automatically does the right thing with it, or you may be stuck with a BIOS that diverts you for months away from the job of getting on with building your OS by behaving differently on different machines. I'd say that if you aren't using real floppy disks, don't bother trying to copy their layout on a flash drive as it's going to waste most of the space on the drive. What you should do is put an MBR on the flash drive so that the BIOS will treat it as a hard disk. Write a table entry into that MBR for a FAT16/FAT32 partition covering most of the disk. Leave a reasonable gap in front of the partition though - I have some flash drives that came with a 2MB gap in front of the partition which is probably there primarily for wear-leveling purposes, those sectors likely being switched round with heavily used ones in the directory to extend the life of the drive.
Once you've defined the partition in the MBR table, you can then simply format the disk in Windows to create the FAT16/FAT32 directory in the actual partition - Windows will simply respond to the details you've written into the partition table. You don't have to do this, but I also put a second partition of my own type in the MBR's partition table and Windows doesn't interfere with it - it simply formats the partition which has been labelled as FAT32 in the partition table (or FAT16 in your case as you're using a smaller drive). Once you've got the disk set up in this way, you can assume that LBA will be available and you can use it without worrying about sector numbers per track, heads or tracks. You can then set up the MBR to boot the FAT16 partition, or to boot your own partition if you want to create one of your own design, or to load the second sector: you can use the gap between the MBR and the FAT16 partition to hold your own bootloader, or you could even stick your entire OS into it.
If you read a sector beyond the end of a flash drive, you can kill the drive, so be careful to work out the right values for your partition - ask someone here to check them if you're in any doubt and state the number of sectors givern for the drive by a hex editor. I made a few mistakes while adapting my OS to flash drives and did read beyond the end of a drive on a couple of occasions, but the BIOS may actually have prevented it from doing so - it simply froze at the point of the call and did no damage, but it could equally have been the flash drive protecting itself that caused the freeze. Don't assume that your setup will be so kind - get someone to check your numbers.
Read the wiki entry on
MBR. You don't have to use anyone else's MBR code - you can simply write your own boot code into the MBR instead, though missing out any BPB that you might be starting your code with with at present. Be careful not to mess up the location of the partition table. Alternatively you can use a standard MBR and label one of the partitions in the table as bootable, and then you can put the VBR (bootsector) of your OS at the start of that partition, complete with BPB if appropriate (i.e. using the one created there by Windows when it formatted the partition for you). If you want your OS to go into a FAT16 partition, you will probably find a gap after the VBR where you can put more load code (or you could even fit a primitive OS into that space). There are many possible ways of doing things. I put my OS in my own special partition after a FAT32 partition and I've written an MBR that can boot either partition if both are labelled as bootable. This setup gives me the flexibility to run my own OS with my own filesystem and to import/export data via the FAT32 partition. I have avoided using the sectors immediately after the MBR, keeping them clear to make it easier to switch to using GPT once it becomes impossible to get flash drives smaller than 4TB.
So, for your early experiments, your best bet is to do one of two things. (1): Write your own MBR code and use it to load the second sector of the disk. You should probably have a partition set out on the disk, but you don't need to use it initially for your OS as there are enough sectors after the MBR to do a lot of experiments with there. Or (2): Use a standard MBR and use it to boot your VBR, while your VBR can then load the following sector(s), again there being enough of them there to do a lot of experiments with. You can then gradually work your way towards having the rest of your OS sit in proper files within the FAT16 partition which your loader can find and load in.
[Minor edit made to correct typos and improve readability.]