I'd chose substrate based of the fish that live in there. Most fish like Angels, like Neon's etc etc come from dimly lit frost stream...so I'd chose something dark (dark brown, black sand or fine gravel).
Just suck out some water from you 10g into 2 buckets: Catch your Mollies put them in 1 bucket, catch your Neon's put in the other bucket, take your plants out split them into the 2 buckets.
Drain the rest of the tank (Turn filter & heat off) take the unwanted gravel out (I love shop vac's for this job that can do wet/dry) and replace with XYZ that you'd like to see in there. Fill up with conditioned water, put plants back turn filter & heater on put fish back.
I'd not suggest mixing...with each gravel vacuum cleaning you'll just mix that up and it'll look less then good over time. I have done this "rearranging of tanks" like described above sooo many time, no problem at all.