Your choice. Most put the disposer in the small sink side, thinking that the small side is used for food prep and gets all the peels, etc. I solved the problem by installing a large single-bowl sink .
I had considered going the large single, but I got too good of a deal on a top-mount Kohler on Craigslist. Best price I could find for anything that fancy new was $325, practically new one for $80.
I guess this new trend on bottom mounted sinks worked out well for me.