Okay, everything I said about OBJ files and Australians I take it back! It wasn't the files that were at fault it was me getting confused lol
Substance Painter has two ways of doing masks for textures - ID Maps and Shader Groups (Materials) and I was trying to use both lmfao.
What I SHOULD have done was imported my Large Storage Crate into Maya, selected Face mode by right clicking and selecting Face from the context sensitive menu and then by left-clicking and holding Shift selected the faces that I wanted to be a different colour. Then I needed to right click and choose Assign New Material from the context sensitive menu:
The I need to select Lambert as the new material and click on the grey thingummybob to choose a different colour. And that's it. I then need to save this model with a different name, large storage crate mats.obj.
Okay, so I'll go through the Substance Painter process of starting a new file so that you all know why I saved that alternate model of the Large Storage Crate under a different name. When you start a new project in Substance Painter it asks you for the mesh that you're going to be using. This is generally a low poly mesh but in my case (at least at the moment) all of my models are low poly.
Now, the first thing you need to do once your mesh has loaded into Substance Painter is bake all of the maps you want under the TextureSet Settings part of Painter: Texture Sets are what Painter uses to differentiate one part of the model from the other, and there are two ways that you can use to differentiate one part of a model from another and use masks to apply textures to them:
1) By using different Materials in your 3D modelling program and importing that model in with all of the Materials or
2) By importing your model with just one material and using an ID Map to differentiate the different parts of the model.
If you don't do this you would need to physically paint the whole model, manually paintint the different parts of the model because Substance Painter will see the model as one big lump. And that would be fiddly and take ages.
Method number 2 is more efficient I think so I decided to go for that one.
So before you do anything, if you haven't imported normal maps etc done using your 3D modelling program when you imported your model you need to use Substance Painter to bake them. For most of these maps it's best to use a high poly model for the bake but all of my models are low poly so I don't need to worry about that so I can check the 'Use Low Poly Mesh as High Poly Mesh' checkbox. Now I haven't ticked the ID map box on the left because instead of using the Low Poly Mesh for that I need to use my mesh with the different Materials assigned to it to generate the ID map.