Hi,
Zooming not working is most likely caused by your JavaScript using relative URL, which doesn't work correctly with SEF links. Either change your JavaScript to be loaded with absolute URL or change the "Set page base href value" option to "Yes - use only base URL" in JoomSEF's Configuration on the Advanced tab.
Modules being displayed where they shouldn't is caused by wrong Itemid being created in your SEF URLs. This problem is quite common but there is no general solution, because it depends on the modules you use and on your menus structure. If you only use one menu item for your VirtueMart, you can set its ID in JoomSEF's VirtueMart extension parameters on the Common tab as Override Itemid, so it will be used for all VirtueMart URLs.