The tactics used will depend on your strategy for VAM, volume of changes and practicality. As usual, what works well in one way may be a problem in another way.
I have a VAR package with alpha textures for clothing which I created slowly over time. At first I kept those textures in my Custom folder and later decided to add it to the fitting clothes VAR to have it all in one place. The first one allowed me quick access but I could delete it by accident, while putting it back in the clothes VAR would be kind of safe but harder to reach and potentially overwritten with a new VAR version. My latest tactic was to pack all the alphas into a single VAR, which makes it safe and easy to share, especially because I make scenes and I don't have now to include that texture file, I can just reference the VAR.
I use clothing presets mainly when playing, so for me the differences in method used for where the texture is located doesn't matter so much. However, for scene making and maintenance it started to make, so I changed to what it is now.
Try out several methods, understand their pros and cons, and be prepared for changes along time. More importantly, make frequent backups of your VAM content.