I don't usually use 1099misc worksheet, just put amount received as income

So, don't you use Schedule C? 

"So, don't you use Schedule C?'

Using Sched C is how you report your client's business activity.

Anyone doing business with your client might not also use a 1099-M to report to them; that's the difference. Your client might do $2 million in business gross income, but as long as no client pays more than $599, your client would get no 1099-M. That doesn't eliminate the need for your client to report Business using Sched C.

Using the tax preparation program to document they received one or more 1099-M means you already entered part of their revenue from that form. It isn't necessarily all of their revenue from their business.

That's the difference between entering 1099-M and using Sched C.