Before, in margin trading, if you are selecting the USD account for example, you can only trade BTCUSD or ETHUSD. Now with the Multi-currency Trading feature, you can trade other currency pairs such as BTCJPY or BTCSGD without having to change the trading account.
All profits and losses will impact the trading account.
A forex transaction takes place first to convert the funding currency to the equivalent market currency before the trade is done. For instance, if your funding currency is USD and you are buying in the BTCJPY market, your USD is first converted to JPY at prevailing forex rates from global forex services before the trade is executed.
Note that one currency cannot act as base and quote at the same time. For example, if you are using BTC as quote currency in ETHBTC market, you cannot trade BTCJPY.