If two instruments are on the same MIDI channel, then they will both receive any controller messages designated for that channel. So yes, if flute and banjo are both on channel 1, the CC10 (MIDI pan) event will indeed be routed to both of them and their pan positions will track together. The only way to pan them independently would be to assign them to separate MIDI channels.
Don't confuse instrument slots in the sample player with MIDI channels, as they're two different things. The sample player lets you play up to 16 different instruments, but each can be assigned to
any of the 16 MIDI channels.
Sometimes, you do want to assign two or more instruments to the same MIDI channel for stacking. But if you want to control pan independently for multiple instruments, each will need to be on a separate MIDI channel. I'm not an E/W user so I can't tell you specifically how to do that, but I'm certain that you can.
None of this depends on your sound card, which would only limit the number of external hardware devices you can drive from the sound card's physical MIDI port. It has no effect on software synthesizers.