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Paland,

I don't understand what you mean by "master project" and "linking" in option 1.

If I understand your situation, I would organize it by making a folder called "Partner Companies" (or something like that). Inside would it I would make more folders, called "Company 1", "Company 2", etc. Inside each folder put all the projects related to that company.

The thing is to keep in mind that you're not trying to take the place of contexts with these folders. Folders are for organization of your projects, to organize what you see in project mode. Many find it helpful to make folders for each major area of focus in your life. It's best to keep it as simple as it can possibly be (and yet still work). It may take some experimenting to find the right level of complexity in your folder structure, one that makes sense to you.

The other useful aspect of folders is that you can focus on a single folder. For instance, if you're having a meeting with Company 2 and you want to see all the current projects that you're doing for them, you could just focus on the "Company 2" folder and wipe all the rest off your screen. Or if you have been slacking on Company 2 and you want to work exclusively on their projects today, focusing on the Company 2 folder would allow you to view only their projects in context mode.