We FINALLY got some rain here, soft gentle rain for a couple days now... in some spots on my solid cover, there's an inch or more of standing water.

When do I pump it off? The instructions with the cover say to leave the water, that it will help hold the cover in place, but we're well above 62 degrees here, so I know the water will grow nasty stuff. Of course it has leaves and junk in it too.

Also, the seams seep a bit, have noticed this during the week it has been covered so far.

I run an automatic cover pump all the time. There are some advantages to allowing an inch or so of water to remain on the cover, but you don't want much more than that to accumulate.