If you're on PC, there's actually a little utility you can use to create a save game state with whatever flags you want, and it imports perfectly into DA2, so you don't have to jump through hoops to get the worldstate you want. There's a forum thread here about it:
http://forum.bioware...save-generator/
As for the original question, I've done Awakening several times with different PCs (never have played the Orlesian warden, but I might eventually). The "best" outcome is to upgrade the Keep and then save Amaranthine, but from a roleplaying point of view, it seems to me that saving Amaranthine is a more personal reaction (i.e., a warden who is more about people and saving them) and letting the city burn is more the reaction of a hardened Grey Warden. They are known, after all, to burn whole cities to stop the spread of the Blight... Even Nathaniel will tell you that you should let the city go and save the Keep (though you can persuade him). You can play it however you like, of course, and justify it however you wish. Such is the nature of roleplaying. 
How it affects later games is actually quite minor. It doesn't affect DA:I at ALL as far as I can tell (though they do mention in one war table mission an "Arl of Amaranthine" and I wondered who in the Void that might be, because as far as I know, the Warden-Commander or whomever was in command at Vigil's Keep was effectively the Arl, but I headcanoned it as being an "acting arl" who was in charge for a while). In DA2, of course, you can get a brief (and kind of stupid) quest where you meet up with Nathaniel Howe in the Deep Roads, and there are some ambient dialogues amongst Fereldens regarding how the Warden-Commander handled the situation (it's been a while since I played DA2, so I can't remember the particulars). There are a few other things (Anders being alive even if he died, for example).
The epilogues in Awakening are complete nonsense, by the way. Most of them were thrown out completely, so I wouldn't worry too much about them. Most epilogue slides in Dragon Age are written in sand on a beach at low tide, so don't play just to get a certain ending slide. It may or may not count for something in DA:I and Trespasser (time will tell how much of that they throw out when they suddenly get a new idea for where they want to take the story), but in Awakening, yeah. Meaningless.