>>Can I have a multi-segmented chart of accounts?

If you mean:

Then, YES.  There are no validation rules on account codes, and you can setup your hierarchy in any way that supports your needs.

>>>Where do I choose a chart of accounts template?

Normally, you will be presented with a wizard after installing the Accounting and Finance module.  

>>>What happens when I update odoo if I have customized the chart of accounts?

Nothing.  Odoo will leave your custom chart intact.

>>>If I customize the chart of accounts, and use multi-segment, what happens on reports?

They work as expected.

Post specific 'I did X, and got Y, and expected Z' if you have further questions.