The filler probably won't darken, especially if you've polyurthaned over it already. They have different color fillers so look for something that matches as close as you can. I assume you're not using any stain because if you are, you could use a filler that will take stain.
The urethane that you used should be fine. Indoor/outdoor is okay - in fact when doing things exposed to sun or the weather, you should use indoor/outdoor. Use indoor/outdoor especially on windows since they are beaten by the sun and then sometimes get the condensation off the glass in the winter.
There are a couple good urethanes - I usually use Flecto. Just don't do like my friend recently did (against my advice) and use a latex based urethane. It raised the grain of the wood and it sticks out in places (which his wife can feel in her bare feet and she's ready to kill him). It didn't help that he didn't sand between coats either. I find I get the best finish using the wool pads that they sell for doing this too.