Using different passwords on each site... and 2FA (which I know Cryptopia offers) would negate a lot of these issues.
As for how the ETC disappeared... either the OP has a compromised machine and the well known Jaxx vulnerability has been exploited after his wallet files were transferred off the machine, or they did something to compromise the security of their wallet (uploaded a copy to online storage or saved a copy of their seed online etc).
Given the long list of sites that their accounts have been compromised on, I'd guess they stored a wallet backup or unencrypted copy of their seed on something like dropbox or email etc... and that account was also compromised.
Hopefully via browser password details he lost the funds on the jaxx wallet. I am also using the Jaxx wallet in my Android mobile but I did not find any loose and hacking problem so far in the wallets. Please keep the seed at the good place where no can to access towards it.
Then there are many ways to keep the wallet secured. You can enable pin for making transaction and then you can go with the Google authenticator also to have the security concerns for it.
Right. Depends on how secured the wallets are kept. Activate google 2FA authendication, Pin for transactions, store the key words written and stored in a secured place and do not store where public view is possible. More over get into the correct URL. Make sure your URL begins with https//:
Activate all the options provided by the respected wallet.