This is something I hadn't come up against before, and thankfully, it's pretty easy.
If you are upgrading flash from one stick to two, you may be pulling one stick from another device. When you do this, there will likely be a partition left on it. Here's how to wipe it so the device will see the slots as contiguous flash.
(copied from here: http://www.dslreports.com/faq/8683 )
It will ask you which partition to erase. Erase the one WITHOUT the IOS on it, usually its number 2. Repeat that for all the partitions except the one with the IOS on it.
HOST1(config)#no partition flash
verify the partitions are erased.
Should see your contiguous flash memory total.