Resolv.conf reset automatically after reboot to the wrong dns

In order to add a new TLD that ICANN doesn't yet recognize (like you are) you have to put a DNS server that considers itself authoritative in the DNS resolution chain. In practice, this means the first hop. In order to use your *.top domain internally, you will have to either point all of your clients at your own DNS server, or maintain /etc/hosts files. One of the two.

As for top.my-domain.com, you have some options. Whichever DNS servers are authoritative for my-domain.com (you don't say) will be able to also serve up top.my-domain.com. This may be your best bet for simplicity's sake. Have your (presumed) DNS hosting service add that subdomain and add the entries you need.

However, hosting a local DNS server is not a bad idea at all really. They're called a Caching DNS server and cache resolved names so they can be retrieved faster than they would be pulling from the Internet. If you add your *.top domain to it, it'll provide all of your needs.

There's a hint about this on http://docstore.mik.ua/orelly/networking_2ndEd/dns/ch06_01.htm:

In other words, an instance of the resolver still queries the first name server in resolv.conf first, but for the next domain name it looks up, it queries the second name server first, and so on.

Note that many programs can't take advantage of this since most programs initialize the resolver, look up a name, then exit. Rotation has no effect on repeated ping commands, for example, because each ping process initializes the resolver, queries the first name server in resolv.conf, and then exits before using the resolver again. Each successive invocation of ping has no idea which name server the previous one used -- or even that ping was run earlier. But long-lived processes that send lots of queries, such as a sendmail daemon, can take advantage of rotation.