Hi bcsteeve,
Normally you would use a cover that was the same or slightly less thickness than the layers that were going inside it. If you had 9"of latex then you would use a 9" cover for example even though the quilting in the cover (if it’s a quilted cover) would add to the final height of your mattress. An 8" cover would probably also work for 9" of latex but the latex would be compressed more and be firmer. If you talk with the supplier of the cover they will be able to tell you which of their covers will be suitable for the layers you are ordering. There is some variation in the thickness of various latex cores so you would need to ask the supplier of your latex the exact thickness of the core you are ordering.
I think that this would be a personal preference and I would base it on your own knowledge of your own sleeping habits. There are many people who are happy with a split queen but as jefmoody pointed out half of a split queen is quite small (only 2" wider than a standard crib size mattress) so for some people you may end up sleeping on the part of the mattress that includes the transition from one firmness level to the other.
Post #2 here includes links to some of the “theory” behind different types of layering and construction but without the help of a knowledgeable manufacturer you are quite likely to end up with a more costly mattress if you try to design your own and haven’t reached the level of knowledge where you don’t need help from anyone else to decide on the best materials and design for your specific needs and preferences. Post #29 here from earlier today would also be well worth reading along with post #15 here.
If you do decide to design and build your own mattress then I would do it for the challenge and learning experience involved because the odds are high that it may end up costing more than you think either in terms of actual cost or in terms of lost sleep if you end up with an unsuitable mattress.
Phoenix