With most set-ups, that should only leave one lead. That should be the earth lead. To check, switch the multimeter to the 'resistance' position and (still with the black lead touching the chassis) touch the red lead against the remaining lead. If the needle moves, there's a continuous circuit and you've got confirmation that the mystery lead is connected to the chassis (and hence to the negative terminal of the car's battery).
If, after identifying the two positive leads, you're still left with two leads, it's possible that there might be one lead feeding directly from the battery, while another is grounded to the chassis. If so, they should both move the needle on the meter. It might not make any difference which is which. (Your radio might only have one connection anyway). If you do want to differentiate between them, simply repeat the resistance test with the negative terminal of the battery disconnected. The lead which moves the needle is 'earth'. The one which doesn't is 'negative'.
If you've not actually worked out which leads go to which speakers, simply place a 1.5V torch battery across the ends of two leads. When you match a pair which go to a particular speaker, you'll hear a 'click' from that speaker each time you put the battery across the leads.
Chris