you setup a batch loop and MPH switches you automatically but you have to be pointed at 12XXX ports.  17XXX for switching within the same algo pool.  You want to switch right after a block is found.  you get paid and you wait for confirm blocks to complete.  Then they are your coins.  Watch for payout mins and transmission fee.   If you send the coins to the exchange for payout it can take 2 to 12 hours normally to return back to your coin of choice.  Some slow trading coins could take several days and you have to watch the exchange, for example maxcoin only pays out best to bitcoin but can takes many days to convert.
Bitcoin is the only coin that is a one way street.  If it goes into bitcoin, it can't get back to the exchange to another coin.  Bitcoin has a high minimum.  see amounts.

Site down is probably overload from all the nicehash people discovering this better site.