I am with a small business redesigning other companies' websites. Often we will host their new website on our Linode account but they will have their email handled with some other provider.
One client had their domain registered with GoDaddy. I changed the nameservers to ns1.linode.com, ns2.linode.com, through ns5.linode.com and did not touch their MX records. There were no problems with the transfer and email service was not interrupted.
Another client had their domain registered with another Network Solutions. I went in and changed the nameservers like last time to point to the Linode, and after a few hours the new site was showing. I then received a call saying that email service was out. Turns out Network Solutions only allows you to set MX records when the nameservers are their own. What I had to do for this domain is change the nameservers to point to the Linode and then configure MX records in Linode's DNS manager.
Is one of these ways the "normal" way of doing it? Will doing it one way affect subdomains? I want to avoid email outages in the future.