You can program with the JB3 installed. I would just leave it off however just to make sure there are no issues at all.
You can update firmware on the JB3 as well. But the JB4 is much much better.
2013 Alpine White F10 535i. JB4 S2, Quad Tip Magnaflow Exhaust, H&R Springs
2011 335ix Le Mans Blue w/ M Sport SOLD
2003 Turbo Cobra 765rwhp/650rwtq 9.77@126 pump gas, lifting @ the 1000ft mark