Welcome to the eCabinets family! It sounds loike you already have a pretty good grasp of the mechanics of eCabinets.
As the others have stated, there is an order to follow.
First, sit down and make out a list of the different distinct cabinet types/styles you produce. For example, closets, bath, kitchen, laundry, bookcases, etc. Use these as your major groupings for the libraries you develop. You may want to further subdivide in, for example, kitchen-base, kitchen-upper or paint-grade, stain-grade, etc. Whatever works best for you, but do organize so you can easily find things.
Second, you must have materials defined before you can use them. As Bryan said, everything is saved as part of the cabinet file but materials exist in a separate database. This does not mean that you can't create materials in the midst of designing a cabinet but it makes it easier if you define the materials you use most before starting to build your library. You can certainly use generic materials and do wholesale material changes to the room.
Next, design the hole patterns for your most often used hardware and associate the hardware with the hole patterns.
If you use any particular edge profiles that are not included with eCabinets, go ahead and design your tools so they will be there when you need them. This is only important if you are using a router or want to show the exact profiles in presentation drawings.
Now that you have all of that stuff out of the way, go ahead and develop your library of seed cabinets. Don't try to create a separate cabinet for every single size you make in a particular style unless you have Part Editor edits that may be difficult to constrain (so the scale accoringly with size changes).
Have fun and enjoy eCabinets and this forum. You will find all the help you want right here.