You can do it in either ways.
certbot certonly will let you enter domain name you want to request certificate and you need to install it by yourself manually. (Paste into Apache vHost and reload Apache etc…)
certbot -apache will let you choose from a list of vHosts (that has domain) and request & install certificate automatically. (Which means less work for you)
However, if you want to request wildcard certificates, run
certbot certonly or
certbot manual .(since you would need to request certificate using DNS validation) and you would need to determine if you DNS provider support API (and if certbot could automate with your DNS provider)