With three RAM sticks, it will be limited to single-channel mode. The extra RAM would probably offset that disadvantage.
If I had to choose between 4GB in dual-channel and 6GB in single-channel, I'd choose the 6GB single-channel setup.
Of course, you could easily fix the situation by purchasing a single stick of the same RAM to make four sticks total. That would be even better -- 8GB in dual-channel mode.