wolf-- we've chatted a little bit about this on Unicornation, but generally I just play the notes in using one sound in a patch cell. It sounds awful, but I can spend time afterwards considering other samples to be loaded into the matrices, building and refining them as I work through the score. Otherwise, I'd play two notes-- stop, go look for the next sample-- play two more notes, stop, and on and on. At least this way I can enter larger chunks of the score in at once-- which turns out to be the fastest and easiest part of the entire sequencing process.
There are times while building a matrix where I'll get an entirely new idea for how the matrix should be built-- and I'll rebuild it as necessary as I go-- changing the vertical or horizontal congifuration to best suit the needs of the music. Sometimes I discover after the fact that one patch just doesn't work as well as I'd like-- so I'll either replace it or add another patch to the matrix-- and hence another series of keyswitches to incorporate them on those notes that will benefit from them the most. Of course, I'll save these edited matrices, and most make for great starting points for other projects. It's not a speedy process because there are so many articulations and controller data in combination to bring your score to life, but a routine DOES develop the more you do it, and you get used to the bit of extra time it takes to put an orchestral sequence together. If you consider that using the controllers and keyswitches are really as much a part of the mixing process as it is of the sequencing process, then perhaps the extra time is not as bad as it may seem at first. I do find some aspects of doing a final mix easier with VI because so much has already been done.
To echo Bruce, overdubbing controller and expression data afterwards is also part of this refining process. If you are using DP5, the track folders will enable you to put different types of controller data on different tracks while keeping your workspace organized. This makes it so much easier to copy/paste/access that info without always having to open the MIDI editor. It also eliminates clutter in the MIDI editor when it is used.
Because VI is so incredibly controller-dependant, I never use it unless I have a completed score either sketched out or clearly parsed in my head. I just cannot work from scratch with this collection-- too much geek-tech right brain thinking distracting from left brain creativity. Maybe others don't have a problem with this, but it really slows me down to try to do both at once.