We are going from SolidWorks to Inventor as our main CAD program and will be converting files to .ipt and .iam. We are moving our file structure into the vault as it is, with some commonly-used components in their own folders. When I convert an assembly, it only grabs the parts that are in the same folder as the assembly. Is there a way to have it look in other folders for components or to have it ask me to locate ones that are not in the assembly folder?
You need to learn about project files. These are files that contain your folder structure and tell Inventor where to look for files at.