For Folding@home, the biggest change will be that instead of the folding@home-client you'll run the BOINC-client instead.
The BOINC "core client" has built in caching, multi-cpu-support, service-install, and multi-project-support. The BOINC-client will automatically download and upgrade science-applications to crunch a wu, just like the normal folding-client does.
You can "attach" to multiple projects if desired, preferences like how many days to cache and resource-share controls when to switch between projects. When one project is down, you'll just get more work from the other projects the computer is "attached" to, making sure never goes idle. You don't need any -local-switch and similar, preferences is web-based with upto 3 different sets of preferences you can group your computers under.
The BOINC "core client" is now a cli, normally running hidden. With the BOINC Manager, a gui-front-end, you can monitor and issue commands to the core client, like attaching to a project, show screensaver-graphics, pause/abort individual projects/wu and so on. You don't need to run the Manager all the time, atleast not when running as service. The BOINC Manager can also monitor/control other computers if you adds a remote_hosts.cfg-file to the other computers...
BOINC will not download work it can't crunch, example not enough memory or disk-space, or too slow computer or not enough resource-share in a project to return before deadline.
Don't know what choises Folding@home has made when it comes to crediting and deadlines, but in most other BOINC-projects the deadline is 1 or 2 weeks.
Crediting is variable based on actual crunch-time, this makes crediting cross-project-comparable, and external stats-sites can make total BOINC-rank and so on.
Only results passing validation is credited, this normally means needs 3 "success" results for a wu before any credit.
CPDN isn't using this method, here credit is instantaneous after a "trickle" is returned.
"Team"-credit will always stay with the team, while "personal" credit will follow a user regardless of part of a team or not.
Folding@home of course will most likely have multiple deadlines, since so huge difference between wu and so many wu-types.
Crediting is maybe based on their normal benchmark-computer, and maybe only sent to one computer just like with CPDN, except when an error pops up that is.