I currently run my Plex Server on a SSD, which I also have my temporary transcode folder on. In this configuration Plex operates fast when delivering data to my devices (Rokus, iPads, Andriod devices, Samsung TV) and also allows multiple devices to stream transcoded content (I've had 9 working concurrently (transcoding) without issue).
So my System looks similar to this
C Drive (OS Only) SATA 1TB
M Drive (Movies) SATA 2TB
N Drive (Music) SATA 2TB
O Drive (Pictures) SATA 2TB
P Drive (TV Showes) SATA 2TB
Q Drive (not in use) SATA 2TB
X Drive(Plex Server Directory
(local Application data Path) 
However, with the Sync enabled, it can consume my entire SSD drive very quickly. With shared Sync, which is great, I can only see this getting worse as my kids enjoy this feature more.
So, I'd like to be able to set a folder where Sync'd files are placed. In my case this could be on my Q Drive drives, as actual speed is for transcoding is now no longer a primary requirement for sync'd files.
Perhaps this is already possible with a registry tweak that I'm unaware of.
I have a similar issue, my root partition is pretty small and plex routinely fills it up either with logs, bif files, or sync files. Moving the transcode directory off my root partition solved most of my problems.
Are you sure you need your transcode directory on an SSD? It seems to me that with 9 transcodes at once your CPU is more likely to be the bottleneck, given ~4Mb/sec only would use up ~36Mb/sec total. If your hard disk can't handle that then it is really really slow.
I used to have Plex on its own independent SATA drive, but found that the application responded slowly, admittedly I was used modified ATV UNITS around the house, before swapping those for Rokus.
But, I found running Plex on in SSD seemed the best option for application performance and transcode operations.
My disk listing above is a little simplified, I actually have all movies on one 2TB drive, as they don’t get played often, but I’ve split my tv shows, so shows applicable to my kids are split over two different SATA drives, adults are split over another two. This way, when I have all three kids streaming to their Android devices, the load is normally split between a couple of drives, as the drives are only operating in read, the performance is pretty good.
When transcoding was happening on a SATA drive, it operates in read and write and has more random operations going on if multiple stream are occurring, writing the transcoded data, then reading it and send that to a client. With multiple you have the heads jumping all over the place. SSD removes that and performs perfectly.
I could move my Plex application again to another driver, but that is a very long process, when copy thousands of small files.
I was hoping that there was a quick fix lurking under the bonnet somewhere that meant I could just set a registry setting to point transcoded Sync files to another drive and folder.
Oddly enough I just posted this same thing, my transcode folder setting works but it only works for streaming devices, not syncing.
I'm happy that the temp Transcode files sit on my SSD as they tend to get removed once the client has finished the streaming operation. Just the sync transcoded/converted to the specific device and sit for ever on my SSD, especially when I can take 50GB of sync'd data with my on the train with my iPad or 20GB on my android device, that alone eats all my free SSD space. Not to mention when the kids do their shared Sync facilities also!
So, it would be great just to be able to allow files that are for sync'ing to be stored elsewhere.
