I personally use a proxy.pac file (which all both Firefox/Chrome support) with roughly the following contents:

    function FindProxyForURL(url, host) {
        var httpProxy = "PROXY localhost:3128";
        var onionProxy = "SOCKS5 localhost:9050";

        if (host.endsWith(".onion")) {
            return onionProxy;
        }

        var proxiedDomains = [
              "example.com",
              ...
        ];

        for (var proxied of proxiedDomains) {
            if (shExpMatch(host, proxied) || shExpMatch(host, "*." + proxied)) {
                return httpProxy;
            }
        }

        return "DIRECT";
    }