This largely depends on your expectations of the market. We will use BTC and USD as examples.

BTC is volatile, and USD remains relatively stable. If BTC is your base currency and is rising fast your other positions will lose value. In this scenario it is often better to trade with USD. If BTC is dropping, but you expect it to go back up at one point, trading in BTC is the way to go.

Market sentiment can change quickly, so stay alert!

In short, it largely depends on your own expectations of the market and your own preferences. 

Good luck, and happy hopping!