I have written several eCart sites now for australian clients all using PayPal Standard as the payment gateway and had no problem getting the cart to recognise AUD
On your confirm page look for a hidden form element called currency_code and change it's value to AUD rather than the standard USD
With regard to your second question that would take a fair bit of custom coding to achieve and I can see logistical issues in terms of tracking orders etc.
You might be better having separate "shops" as subdomains i.e. mygreatshop.mydomain.com, myothershop.mydomain.com etc. but if you lay out your business plan you might get better suggestions