As a rule all prices entered by admin are net prices ie price without tax. Tax is always applied afterwards.
You can set whether your clients should see prices inclusive / exclusive of tax.
If you disable tax for a company, those users will not see it anywhere and orders in admin will show tax = 0
You can set different tax rates per company.
All shipping prices by default should be entered as net price. Tax is applied afterwards.
You can apply tax to shipping but it will require company tax to be enabled for it to show.
If you modify a shipping rate after an order has been made any tax applied will depend on whether company tax was enabled or not at time of order.