Hi Chris,
SharpCap is aware of the different co-ordinate systems and deals with the conversions where necessary, so in this sort of situation we have
* Target co-ordinates in CSV are J2000, mount is JNOW - SharpCap converts J2000=>JNOW before sending target to mount
* Plate solve results are J2000, SharpCap converts those to JNOW before sending them to the mount for the SYNC
* Re-goto after plate solve - again SharpCap sends the JNOW co-ordinates to the mount
So, the mount display in SharpCap (and what gets written to capture settings files, etc) will always be in the mounts natural co-ordinate system.
It all works, providing everything really uses the co-ordinate system that it claims to (or should). So, things would go wrong if you entered the target co-ordinates in JNOW, or if somehow you set up your mount to claim it was working in J2000 when actually it was JNOW (it's possible to configure EQMOD to do this)
cheers,
Robin