If your bot is a dll that is going to get injected into a target process then I would recommend this method to you:
1) Use a backend web login with your loader which identifies a user
(The user has to register his HWID either through your website or first startup - up to you.)
2) Then you need a little script in your backend web app which streams your bot dll directly to your Loader (don't save it on disk just keep it in the RAM), encrypted with the users HWID saved in your database. (Just a simple download script)
PHP Code:
//Pseudocode
$botModule = file_get_contents('bot.dll');
echo encrypt($botModule, $hwid);
3. The loader decrypts the dll which is only possible if the PC of the user has the HWID which is linked to his account he is using.
Your bot dll can still be extracted when it's injected though, so in case you want to protect the module itself you have to hide it. I think you have to rewrite the PEB or sth like that, can't remember -> research with google by urself. But it's important to notice that there is no 100% protection if someone want to crack your bot he is able to!!!
Sry for bed englando it's very late