I found the answers at the BitTornado site:
"Manual Announce" forces the client to reconnect to the tracker. This is useful if your connection dies.
"External Announce" lets you connect to another tracker hosting the same torrent set, bridging the two trackers and allowing you to share data with both sets of peers.
"Finish Allocation": As mentioned before, BitTorrent downloads randomly though it fills disk space linearly. The Finish Allocation function fills the disk space in the background until all necessary disk space has been acquired. This is useful for various reasons, including re-ordering the data inside a torrent so the contents of a complete file are in the correct place and the file is usable.