Once you have setup quoting by uploading your parts list, D3M still doesn't know which parts to assign to icons and connections in your projects. However, once you assign a part to an icon that you have added to a project, D3M will remember that decision and quote it for you and your colleagues automatically next time you use the same icon. There is no need to do any setup. Build your first quote by manually assigning parts to icons and connections, and the next quote will automatically quote for all the icons that you have quoted before.
NOTE: Automated quoting does not yet work for connections
How to override automated quoting
If you have icons that you frequently attach different parts to depending on the solution you are designing, you might run into a situation where D3M seems to be randomly selecting from those parts that you frequently quote. The best way to mitigate this is to create custom icons for the different situations that you deal with. Just click the icon that you want to make copies of in the library and click the Create Custom button at the bottom of the library. When you create the custom icon, you can lock in the quote parts that you want to be automatically quoted, or leave it blank and let automated quoting take over.