I just went through this with new bulkheads in my boat. Here is a pic of how it turned out.
The front of the hanging locker is the original teak. I sanded it and then just varnished it. The two sides of the hanging locker were rotted from leaks around the chainplates that attach to it. I replaced them with birch ply stained with two coats of Zar's Natural Teak color.
I wanted a very close color match so I used a piece of the birch as a test. I bought 3 different stains that I thought might nail the color. I then stained 3 small patches of the birch with one coat of each stain. Then did three more patches with two coats of each stain. Finally I varnished them all. The patch with two coats Natural Teak stain and varnish turned out almost an exact color match to the refinished original teak.
In regards to staining before or after sealing the wood... I did notice that 3 days after applying the stain, it would still shed some of its color onto items it touched. I did one more dry fit after staining and before the varnishing...the stain rubbed off onto some of my newly painted surfaces inside the boat.
My complete refit is taking completely too long!