You can create folders in Safari really easily on the iPad. Here's a walkthrough..
Bookmarks Bar Feature
"The other useful navigation feature is the Bookmarks bar, similar to what's in the regular Mac version of Safari. Adding bookmarks in iPad version of Safari is similar to how you add bookmarks in the iPhone and iPod touch, but adding URLs to Bookmarks bar may not initially obvious. So here’s how it’s done:
Tap on the + button to add your selected URL. The Add Bookmark panel will pop-up.
As you should know, when you save a bookmark, you can edit the typically long title of the page. If you plan to add several bookmarks to the bookmarks bar, you should keep the titles fairly short.
Now at this point, you probably will not see a folder for the Bookmarks Bar. Tap on the default or current folder under the name of the URL. You should be presented with a list of folders, including one called Bookmarks Bar. Tap on to open it and then click Save.
To edit the bookmarks on the bar, tap the book icon; tap Edit and select Bookmarks Bar. And then finally, click the Edit button again to select when bookmarks you want delete or re-arrange.
You can also create folders within folders for the Bookmarks Bar, just as you do with the desktop version of Safari. When you tap to edit the bookmarks bar, there is a ‘New Folder’ button on the left side of the panel. Create a sub-folder which will appear in the bar where you can add URLs as described above."
Once Bookmarks are saved, you can also move them between folders if necessary.