Yes, you can have multiple working targets in the same Scratchbox installation (mine has Diablo, Fremantle, and Harmattan targets set up). I've started out with a Fremantle SDK installation. IIRC, the Harmattan SDK installer "upgraded" my existing Scratchbox installation just fine (both the Fremantle and Harmattan targets were working OK). I've installed the Diablo target more recently by setting up a new target manually (via sb-conf).
libfakeroot: invalid port number in FAKEROOTKEY