It would probably have been better to ask a Mountain Lion question in the forum for Mountain Lion instead of the one for Snow Leopard, but I can at least make a couple of suggestions.
Working from the bottom to the top, in Mountain Lion, you have to hold the Option key while selecting the File menu to see the Save As… item.
In the newer versions of Preview, you can have multiple documents in one window, with the thumbnails for all of them in the sidebar. If you grab the thumbnail(s) for the second document and drag it up toward the first, you will see a divider between the two document as the pointer approaches the first and a "+" sign will appear next to the pointer as it crosses into the first document. If you release the mouse button when the "+" is showing, it will merge the two into one document.
You're right, I thought it was just under the merging with preview section. I now see the Save As button, but it still doesn't merge them, it just means that when I open the new file it open both and automatically puts them in the same window, which doesn't work when they are opened in Acrobat or iBooks. The drag and drop to create folder part doesn't seem to work, but I know what you mean. Anyways, it was much easier downloading some small merging software. Thanks anyway.