The cPanel IP Deny Manager does modify the .htaccess file but that is not the only purpose of the .htaccess file.
If you decide to manually modify .htaccess you should do it with caution and only after reading some information on the .htaccess contents/format as you can cause problems with accessing your site if you mess up the file. Here are some references:
http://httpd.apache.org/docs/1.3/mod/mod_access.html
http://httpd.apache.org/docs/1.3/howto/auth.html#access
You should make a backup copy of your .htaccess file before you make changes so that you can restore the original if things get messed up.
You might also try entering some IP addresses using the cPanel IP Deny Manager first to see what it enters into the .htaccess file, then follow that pattern for manually adding additional blocks. Doing it this way should keep the .htaccess format compatible with what cPanel is expecting.
I would still recommend using cPanel IP Deny Manager to avoid unexpected results. It may be a lot to enter but it's not something you'll be entering frequently.
Regards,
Rich