there is a Bus Station just after the Israeli Immigration in Beit Shan Border Post where you can ride to various points in Israel, some of these buses are in consotium with the JETT Bus comoany of Jordan and they Ply the Amman to Jerusalem Route and vice versa, just show them your Jett Bus ticket to Jerusalem and you can ride them at no extra cost.
If you are in a package tour like us, your tour guide will meet you after the Immigration and customs area (it can be a rather long wait as Israeli security is the strictest in the world) and then escort you to your designated tour bus or van and you can then proceed to your destinations.
From Jerusalem Central Bus Station, take Bus Number 966 or 961 to Beit She'an - Binyamin Mall for 71 NIS (1USD = 3.7NIS). The bus leaves at 8:15am or 10:00 am, arrives at 10:21am or 12:02 noon. At Beit Se'an Bus Terminal - Binyamin Mall - walk through the old square, the citadel should be on your left as you walk toward Bet She'an National Park, turn in at the first shopping strip mall to find the entrance gate. Google the map.
Check www.egged.co.il for up-to-date schedules and fares;