I think it only works with the stock keyboard.

Sent from my SCH-I605 using Tapatalk 2

 

It has worked fine with all the keyboards I've tried (which haven't included SwiftKey yet). But I use it all the time on Hacker's since I made the keys too small to hit accurately with fingers. The only issue is that the S-pen has to be pretty perpendicular to the screen so that the nub makes good contact, which sometimes makes me miss letters on the other side of the screen when I'm using in landscape.

Just realized that you are probably referring to handwriting input, rather than just using the S-pen to hit the right keys.

 

It's not handwriting, but you can use the S-Pen on Swiftkey Flow to spell out the words by tracing from letter to letter (like Swype).

 

I just tested it out. It does not work, there isn't a handwriting mode in swiftkey 3 that I can find.