I'm going to be in Israel, and want to visit Syria and Lebanon. I can get a second passport for Syria and Lebanon, but I already have Israel stamps in my primary passport. I was thinking I can go overland from Israel to Amman and then use my second passport to fly to Beirut and then travel overland from Beirut to Damascus. I'm assuming the border check is easier there than coming from jordan? Also, if I did do this, I assume I would fly out of Amman on primary passport and enter Beirut on the secondary passport, or would Beirut notice that I have no exit stamp?

Depends on the border guard. On the whole, I think you'd be best off flying from Israel to Amman and then using your secondary passport starting there. As Israel is known to stamp separate papers on request, this would be the most invisible way to visit both Lebanon and Syria after being to Israel. Really, though, I think the ideal solution is to simply reverse the trip and go to Lebanon/Syria first, then Israel afterwards on this trip. Traveling in and out of Israel and later attempting to get into Syria is a recipe for refused entry.

yea, i agree, it would be easiest to start in Beirut with the second passport, unfortunately, I can't do this. Other concerns that popped into my head for flying amman to beirut, and using my primary passport (with the israel stamp) to exit amman, and my blank passport to fly into beirut:

a) will Amman, when i fly out, be checking that I have no Israeli stamp in my passport (because using the second passport to leave Amman would cause a problem because it would show no entry into Jordan)

b) arriving in Beirut airport, will it raise any concern that I don't have an exit stamp (this is less of a concern for me because flying out of the U.S. and E.U. I've not received exit stamps, so it's conceivable that I could've come from any destination).