I'm going to assume that you are generating your prints/outputs using the "fabrication outputs" under the file menu and NOT using an output job in your project. If so, you can configure the fabrication output settings by selecting "Default Prints..." in the same file menu. In the dialog box that pops up, find the print that you wish to edit and select the configure button at the bottom. You can then edit the layers, colors, object types, etc for drawing shown. It might be confusing at first, so it will take a little time poking around in there. Once the prints are configured, you can just generate them using the "fabrication outputs..." menu under the file menu. You may wish to generate each drawing type independently as opposed to using the final drawings output option.
free_electron's information covers the case where you add an output job file to your project. That can be added by selecting File > New... > Output Job File. The output job is more powerful, so you should investigate that method as well.