Checkout and shopping cart module.

Have shopping cart displayed on left hand side.
Click on proceed to checkout.
In checkout / login / registration screens the shopping cart is still displayed - this is unnecessary when in checkout.

This maybe something I would want to control in my Joomla template as I may not want to display either of my margins when in the checkout.

In the configuration of HikaShop there is the option "Force a menu on the checkout" in the tab display.
In this option, you can select a menu which will be applied on the checkout instead of the previous menu. That way, you can personnalize your modules to not be displayed on the checkout page.

does this mean i would have to create a checkout article or a hidden menu?

A hidden menu yes. You can set it to a main menu which is not displayed in your template so that it doesn't appear if you don't need a link to it visible.