The easiest (and most reliable) way is manually, at this time. Just load Content Manager, goto Online Storage, PS Vita System > Online Storage (not vice-versa), tap Select All, then Copy. Should only take about 5 minutes (via WiFi) - but could be slower if you have saves like LBP (which is 70mb)...
Last night, I was going NUTS after reading your first post. It took me a good 15 minutes to open up Content Manager on my own.
I just thought it would be in settings or Application Data Management. I had only used Content Manager one time prior to copy over some movies, so I did not think about it for Save Games right away. Wish I had seen this sooner. Thanks.
So is it a bug that choosing Automatic Upload does not stay?
Mutant Blob is a great game, played all the way through and it was well worth it, amusing and the puzzles are not that hard so it adds up to a nice flowing easy to play game.
Seems very good so far. Got through the college levels and really digging it.