As far as I can tell, the only neg on the KD8CEC software is that "apparently" it does not read the encoder reliability fast enough to allow you to use a digital cnc 100ppr knob you can get on ebay for $14. There was a thread that "some ubitx firmware" read the encoder fast enough to respond to 100ppr. (check ubitx.net for a discussion on encoder).
however, for the standard encoder that comes with the ubitx kit, KD8CEC reads it fine and you will be happy.
The other thing to do the upgrader sooner than later is that on first install, KD8CEC records the criitical values (OSC, BFO, etc). You then have the ability to do a "factory reset" to these values if in the future you ever mess something up. So do the upgrade before you start "tuning"...