If you've already applied one coat of spar urethane over stained wood can you still put another coat of stain if you want it to be darker?

No. Once you have varnish over the wood, stain will not penetrate. You can get colored varnish and try to darken it that way. I would get a lighter shade than what you want. All the varnish stains are put on white pine to get the samples. Since the wood is already stained, putting the color you want on now would cause it to be too dark.