How can I give a customer multiple options on one estimate without it automatically adding everything together at the bottom

The only sure way to do that is to enter "0" for Quantity for each item. I do not think you can hide the total column or field from view.

Clearly label the options as options. When you get approval and convert to an invoice you select only the chosen options.

When we have multiple options, we create separate estimates for each one. 

If you really want them on one estimate, you could use subtotals. Here is an example of how we did this for one client:

You will still have a total at the bottom. One workaround to get the total to be zero (or just equal to some base estimate) would be to add a markup/discount line that is the negative of the extra costs.