Key frame alignment between bitrate version is required for multi-bitrate streaming. We recommend Expression 4 Encoder (though others such as Handbrake will probably work). Take a look at the Expression 4 Encoder presets in this article:
Wowza supports multi-bitrate (ABR) streaming to Silverlight client (smooth streaming), iOS devices (cupertino streaming) and Flash HTTP (sanjose streaming) directly using .smil files. Take a look at the multi-bitrate section of the vod tutorial
The app/web server is used mostly to send players to clients. The client, e.g., a Flash player running in a browser, is what connects to Wowza. A web server serves static players, the app server can do all that it does to form the player as neccesary per request.
You can communicate directly with Wowza over http by creating HTTPProviders