We have revised our item to spend 5 days near Krabi after we do Siem Reap. Do we have to fly back through BKK? Id prefer direct. If so, can we get to an island that night or better to stay in Krabi town by the airport? We will be looking into Diacovery Pass.

Your options are through BKK or KUL, the former being the most logical choice.

What island are you trying to get to from Krabi?

I believe it has to do with this itinerary.

OK, the OP started out heading for Ko Phi Phi, then adjusted itinerary so that Ko Lanta is now the frontrunner. Frankly, I think Ko Lanta sounds like a better choice for him, esp with a tiny baby. So then...how to get REP-KBV to Lanta in one day.

OP, I think you are going to find that this is where Bangkok Airways (and the Discovery Pass) is less than completely helpful to your cause. To wit, possible connections just using PG (no nonstops REP-KBV exist on any airlines):
Option 1)--REP-USM-KBV gets you in too late, likely an overnight in USM before continuing on to KBV
Option 2)--REP-BKK-USM-KBV is just Ugh! with 2 transfers, plus a USM-KBV flight on a small ATR. No, just no.
Option 3)--REP-BKK-KBV possible taking the first flight out of REP, long connection in BKK, arrive KBV too late to continue/overnight there. Onward to Lanta next morning. Also not the ideal choice though maybe a backup plan.

You would be better off using PG (and maybe the Pass) only for the REP-BKK leg, then picking up a different airline (my preference is TG) for the onward. Doing this and taking the first PG flight out of REP would get you into BKK with enough time to catch the early afternoon nonstop to KBV, arriving before 3 pm, then get ground transport directly to Lanta (2 hours-ish) arriving well before dark.

Although there is also a Thai Air Asia (FD) flight in the afternoon which is cheaper, I like the TG flight because (a) schedules are more reliable (b) the TG flight leaves earlier than the FD flight, giving you more daylight to get to Lanta and (c) PG and TG interline baggage so you should be able to check baggage in REP and not have to deal with it until KBV. You would only have to go through transit immigration in BKK (for certain domestic airport destinations including KBV) and Customs clearance would be in KBV. With FD, you'd go through regular Thai entry immigration, pick up baggage at PG carousel, go up to FD to check-in, then back through exit immigration which takes time and hassle and it isn't fun for anybody much less carrying a baby.

From KBV, you'll need to research various means of ground transport to Ko Lanta. If you cannot get a shared van/minibus, then consider springing for a private car pickup at Krabi airport.

jiejie makes a salient point that I've thought about but not put down: Just because you have a discovery pass does not mean you should shun TG (FD, DD etc) flights if they are more advantageous.