Quick one - is upgrading the extentions via Magento Connect the same as applying the SUPEE patches?
No and Yes.
No, upgrading extensions is not the same as applying SUPEE patches.
Yes, if you are using Magento Connect to upgrade Magento to the latest version AND THE SUPEE PATCHES ARE INCLUDED IN THE VERSION UPGRADE, the upgrade is the same as applying the SUPEE patches.
You must check to see what SUPEE patches have been applied to minor Magento upgrades, in versions previous to 1.9.1, often the upgrade did not include some or all of the SUPEE patches and you would have to patch every time you upgraded Magento until the SUPEE patches were included. It seems that Magento finally got Security Religion in 18.104.22.168 and is starting to make sure that the SUPEE patches are all applied to the latest Magento version release available. We'll have to see if they continue this in future, but it would be a vast improvement over installing 22.214.171.124, fully patching it and then finding you upgraded to 126.96.36.199 and were no longer patched because the interim patch had not been applied until 188.8.131.52, and had completely reopened all the security holes.