In a sense, it does matter where you put the rewrite rule. It should go inside the mod_rewrite configuration
RewriteRule ^.well-known/(.*)$ - [L]
[... other rules?]
But before you do that… are you sure you need to do that? The article you linked says:
To play it safe, rename your .htaccess file (to something like .htaccess_OFF) in order to turn it off temporarily. Then, install the certificate. Once installed, you can rename the file back to .htaccess.
Do you know for sure that disabling .htaccess breaks your site? In any case, make a copy of your .htaccess before editing it so you can quickly revert back any change in case your site stops responding properly.