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If you scan the public_html directory on the main site then it will probably scan all the sub-sites, it just depends on how your sites are structured on the filesystem.
The most important thing is to get all you sites clean at the same time. If you scan all your sites, and remove all the malware, and then scan all your sites again, and they are all fine for a little while, then the problem may not be coming from any of your sites. This malware could be spreading from a site on another account on that server. In that case you should probably move all your sites to a move secure server where they will not be exposed to cross-site contamination from other users.
I do offer Super Secure Hosting for $12/month per site. I could host all 4 sites for $44/month and they would never get hacked again. Let me know if you are interested and I can help you move your sites over to one of my Super Secure servers.
