Limits protect your allocation and, more importantly, protect your clients from each other.
WHERE THEY ARE SET
Defined in the package, and adjustable per account under WHM > Modify an Account.
WHAT TO SET
Disk quota. Keeps one client from consuming your whole allocation. Set a figure you can honour. Bandwidth. Less critical for most sites but worth setting. Max Email per Hour. Important. One compromised mailbox sending spam damages the sending reputation of every account on the server, including your other clients'. Max accounts, databases, subdomains. Keeps packages honest and gives you an upgrade path.
WHAT NOT TO DO
Do not set unlimited on anything. Your reseller allocation is finite, and "unlimited" simply means the limit is discovered at the worst possible moment, by everyone at once.
MONITORING USAGE
WHM > Account Information > List Accounts shows disk and bandwidth usage per account. Check it periodically rather than waiting for a complaint.
WHEN A CLIENT OUTGROWS THEIR PACKAGE
Contact them before they hit the limit. A proactive upgrade conversation is far better received than an account that stopped accepting email over a weekend.