On critique of Dilt's neurological levels, I've read claims that real logical levels is when a higher category includes and transcends each category of lower level within that higher category, and so on. And that moving up each level is "going meta". And, that is different from hierarchical levels like CEO to manager to technicians, etc.

Well this principle seems very powerful and helpful for getting organized in office, home, etc. For example, organizing rooms in the house, the filing system in the office, and bunch of different data. Also seems very useful in organizing thoughts and seeing how others think.

The problem I feel, is that there are so many different ways to logically categorize.(which I think is why using tags and database type of storage of information is so useful due to the flexibility of ordering) It would feel great to develop better ways to organize for practical usefulness using logical levels though.

Any thoughts or help on most efficient ways to apply logical levels for organizing life?

In general, Don't!

In specific, when thinking about a given situation or making a given change, address each level, because in doing so, you will produce the positive effects that logical logical levels are designed for.