We are a two-Kobo home, as well. We use one kobo books account, one (Adobe Digital Editions) ADE account. and then transfer our books using ADE or Calibre, rather than syncing through the desktop app. We can have different books on different machines. We have two computers.
Calibre (
http://calibre-ebook.com/download) would be your best bet with only one computer because then you do not have to authorize your Kobo with ADE each time you switch readers. There is a limit on how many authorizations you can have with ADE and even though you are reauthorizing the same devices over and over, it may max-out that way.
You cannot use many of Calibre's amazing features with the ePUB books you download from kobo books, without removing the (digital rights management) DRM, but you can easily use it to transfer the books onto your device. You may want to look at the help files if you have trouble figuring out how to transfer books--though it is easy peasy if that is all that you are doing.
To download the ePUB books onto Calibre, click on the download link, and then rather than accepting ADE as the program, navigate to the calibre.exe file. On my Windows 7 machine, the path is "C:\Program Files (x86)\Calibre2\calibre.exe" If you have any Windows install, it will be some similar location. Not sure about MAC.
Once you find it, check the box that indicates you will use Calibre to open all ePUB books.
PS: Unless you do a factory reset (under advanced settings) or send your purchased/I'm reading books temporarily into the trash and resync (remember to restore them from the trash if you do this) you will have two versions of your books if you add previously purchased books through Calibre without deleting the books added through sync. Best bet might be to use this method with only your new books if you are technology impaired.
When I figured this out, I did a factory reset and replaced the sqlite database (see other thread in the sticky section). I then did the remove to trash and sync with all of my books (followed by a reverse of the trash part so all of my books showed up again in my library on the kobo books site). Then I did the Calibre/ADE transfers and had what I considered a cleaner machine.