Heh, you have no choice but to use root. There's always a risk when using root. There's teh 0.1% chance there's a keylogger on your comp, and someone can get your root password to DDOS from the box. But, its the same for passing any passwords around i guess.
Unless, of course, you setup a reseller account with root, that has 'unlimited' everything, and you just make accounts via that.
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sudo is your daddy. Any box I admin, root is not allowed to login interactively via SSH. A standard user is created then when necessary, sudo is used to obtain root priveleges. This way you're not transmitting any root password information over the wire. Yes, ssh is encrypted but its not worth the risk in any case.
it's not really a problem, but using setting up sudo/sudoers does help to make it all the more secure if you are using SSH.
However as far as WHM is concerned, you certainly can create a reseller account and add all the privileges that the root account has. That can help you from having to use the root account to login to WHM. (But you can actually restrict it and only allow some of the most commonly used functions to limit liability if that login is compromised.)