Why do you want to use a stacked sequence structure?
I suspect that the majority suggestion on LAVA would be to convert the flat seqs to sub-vis. If they are old and work, don't mess with them; especially if you aren't touching the code inside them. People usually use flat seq structures to enforce order of operation and a seemingly simple change can break things badly. They did this because they don't understand dataflow which means they don't know LabVIEW and that means there may be other monsters waiting to bite you.
If the flat seqs are large (complex) and need to be modified, it might be better to create a sub-vi. Within the sub-vi, they can be converted from a flat to a stacked seq structure and then finally to a case structure that can be wrapped with a while loop and some shift registers to be turned into state machine. You can even use a diagram disable structure to leave a copy of the flat seq in place as you refactor. If something doesn't work, you can just use the old code until you have time to 'do it right'.
If the flat seqs contain locals or property nodes that modify data not related to the code within the structures, you've got a whole big, ugly, nasty bag of butt hurt that can't be fixed with sub-vis or get better by adding a stacked sequence structure. The block diagram of your top level VI may look nice, but the next person looking at the code won't be any happier than you.
When I open a piece of code that contains nested sequence structures, I become instantly upset to my stomach.
My choices in order of preference:
1. State Machine
2. Flat seq structure
3. Anything else ( )
4. stacked sequence structure
P.S.
Remembered this from the NI Idea Exchange:
http://forums.ni.com/t5/LabVIEW-Idea-Exchange/Splitting-and-exiting-flat-sequences/idi-p/1535798