Somehow I was able to do this once before, since most of my bookmarks are on iPad now. Been trying to sync them again from PC so IPAD has ALL my bookmarks and it's not syncing the new ones. Went into iTunes on my PC and it says that all my bookmarks will automatically sync to iCloud so can't figure out what else I can do. It should be done automatically every time I sync iPad to PC! Any ideas?

When you updated to iOS 5, and updated iTunes, you should have ended up with an iCloud control panel (or something with a similar name). Someone who actually has Windows should be able to give you more details if you need them. Make sure you've enable your bookmarks syncing there. I'm pretty sure Windows users can select IE as a source.

On the iPad you need to go to Settings > iCloud; sign into your iCloud account if necessary, and make sure bookmark syncing is turned on.

This all supposes you already have an iCloud account. If you don't, the you should be offered a choice of creating one somewhere along the line. It should also allow you to use your existing iTunes account ID and password. Up to you, but if you're the only one using that iTunes account it keeps things simpler.