Now, I've never tried to schedule or set up programming for any convention of significant size. (My one experience was for a con that never got off the ground, nor got to the point where we were actually trying to program our one track). So I'm talking without any experience, but here is how I might (in very broad strokes) schedule a Worldcon sized event -- that is a 3000-6000 person convention that runs over 5 days, with the first and last day being only half-days.
The first day, have only some activities open before noon or 1:00pm. These would include registration, and possibly children's programming, child care (two different things), and possibly the con suite. Dealer's room, art show and other related exhibits could be opened as long as there was sufficient time to set them up.
I would then gradually start programming in the afternoon. Probably only a few tracks going before 3:00, and then full tracks going until 5:00.
The last day would be similar but reversed, with full programming from 10:00 until 1:00 or so, and then a few key items against Closing Ceremonies.
On the middle days, I'd program fairly fully from about 10:00 until 5:00, with about a half-load or less from 5:00 until midnight or later. Much of this would depend on facilities and access. I'd also try to have special events each evening probably starting at 7:00 or 8:00, with even fewer main programming items against them. Evening events would include Opening Ceremonies, Guest of Honor special presentations (possibly all serially in the same evening, if there was enough time), the masquerade, and The Hugo Awards for a Worldcon.
Alternate programming, such as gaming, visual media programming, filk concerts and panels, etc., would make up the bulk of the programming against the major events. Children's programming and child care would probably need to run during these hours as well.
As far as how long to schedule panels, I might do what was done in 2005 in Glasgow by having a mix of 75 minute and 20 minute panel slots, and possibly have some 50 minute slots first thing in the morning and in the evening. One thing I would make very sure to emphasize is that the panels do not run back to back. If the start time is one hour apart, the panels are 50 minutes, and if it is an hour-and-a-half between panels, the panels themselves run 75 minutes. At a large event there needs to be time for both panelists and audience members to move from room to room between panels.
Of course, as I said, I've never actually done anything like this, so I'm probably just talking out of my hat.