Yvoire is the size of Place de la Concorde, at most, so you won't have problems to move around and see everything. You will have to walk - they don't allow everyone to take their cars inside the walled city, so you must leave your voiture in the parking lot outside.
To get to Yvoire from Geneva, we enjoyed a leisurely ride along a country road (D25) that passed through some lovely little villages to get to Yvoire, it was barely imperceptible that you were passing from Switzerland to France as there was no border guard, at least not that day. Remember to take your passport though if you are coming from Switzerland and remember that the currency switches to Euro.
Michelin's website takes you along N5 which is a slightly larger and faster road but if you have the time, I'd recommend D25. I don't recall exactly how long it took but it's about 30 kms so I don't think it took much longer than 30-45 minutes from Geneva. As with most of the driving on this trip, we found that directional signs were excellent, we rarely consulted our map except to figure out if we wanted to take the highway or more scenic routes.
Yvoire is pedestrian only so you park in the pay parking lots, you pay after you are done with your visit.
The Lac Leman (lake) is long and narrow, and its Northern side belongs to Switzerland, while the Southern section is France. It is a good idea to drive around the Swiss part of the lake, leaving from Genève and passing by Lausanne, Montreux and the Château de Chillon. Yvoire is in France, but it is very close to Genève. I believe a car is the fastest way of getting there, and since it's just a very small village, you'll probably want to go ahead and see other towns that same day.
Whether you go by car, train or boat, as you see Yvoire is just a tiny little town.
By boat you arrive on the northside. By car on the south side. A large parking is available at the city entrance