We chose to fly one-way to Quito ($365) from Los Angeles and figure things out from here. This is how things have shaken out: We are going to fly from Quito to Santiago ($420) one way. The same ticket in the States would cost about $500 because there are no student discount fares out of Ecuador. We had the option of overlanding it to Tumbes in Peru and then flying via Lima to Tacna and overlanding it from there to Santiago. While traveling this way would save about $200 each, we have chosen to avoid the hassles of transporting our bikes and all our luggage more than once.
That said, I wish we had bought our tickets to Pta. Arenas while still in the States, as the same ticket here costs about $200. The other option is to take the ferry through the fjords from Puerto Montt, but those tickets are running about $600 for a cabin, as it is coming into high season for Chile.
We will probably hold off on this decision until arriving in Santiago as things there may be less expensive. We don't want to forsake the ferry just yet.
In all, don't worry about accommodations coming into Quito. The airport is very mellow and it is easy to arrange transport and accommodations from there. You should be more concerned about LAX, where our bags were almost snatched.
A great place to stay in Quito is La Casona, located in La Floresta, a wonderful residential neighborhood. Prices are about $6 per person per night. It is a beautiful old Spanish colonial house run by some expatriates from Argentina. Muy tranquillo.
As we predicted, our biggest challenge has been moving around our mountain of gear. I can't wait for the day when everything is self-contained on the bicycles. We did bring the full accompaniment of mountaineering gear, but shipping this to Santiago and onward to La Paz and Huarez in Peru seems cost-prohibitive. Good-quality mountaineering gear can be rented inexpensively in Quito. The same is probably true in Bolivia and Peru, although we've heard that the quality is unreliable. A good motto: Maximum pleasure is inversely related to your amount of baggage.