Both are really great guitars for their price. It's kind of unfair for me to compare between the two but really I have only good things to say about both. But if you want to compare I may be a bit bias (Sorry Sterling) as EBMM guitars are definitely more superior. For instance between the JP6 and JP100D I'd say the most noticeable differences are the neck, floating bridge and piezo.
The Neck
The neck on a JP6 feels thinner and the finishing really makes it a fast neck. The stainless steel frets feel great compared to the Sterling's nickel (?). Both are really comfortable to me.
Floating Bridge
The floating bridge wins my vote the most. If you'd ask me why I love my JP6 it's because of the floating bridge. I was used to a Floyd before but when I got my Sterling it sort of felt rigid and the way it is secured (small bolt on the side, secured with an allen key) makes it feel a bit loose, didn't use it much. Then when I got my JP6 and tried the tremolo I found myself using it like the time I used a floyd. You can feel and hear every movement of the tremolo bar and it's tight like it's supposed to be. Lastly the plate cover on the saddles make it a comfortable place to rest your hand while playing.
Both my JP6 and JP100D have excellent tuning stabilities though!
Piezo
My music style incorporates a lot of acoustic and distortion sounds and having this feature along with the Mono & Stereo jack and switch makes it really easy to switch between the two PLUS the piezo sounds superbly awesome.
I haven't been able to compare the sounds between the two but I can say the JP6 has much more clarity and sustain. You can always look up a tone comparison on youtube.
As I said, both are well worth their price. If you're on a tight budget the Sterling guitars are magnificent instruments for the < 1000USD range but if you add a little more you can get a used JP6 now for 1500usd with hardcase included.
This is just from my personal experience. Hope it helps!