One of my 1099 vendor received payments from a unrelated checking account. how do I add this amount to thier total paid

Let's write a check to record the amount received by your 1099 vendor, @elisa7. This way, it will add to their total paid figures in the program. I'll guide you how. 

1. Go to Banking from the top menu.
2. Choose Write Checks.
3. In the Bank Account field, select the unrelated checking account. 
4. Choose the vendor in the Pay to the Order of box.
5. Enter the No., Date, and Amount. 
6. Select either Expenses or Items tab to enter the necessary information. 
7. Click Save & Close.

The screenshot below shows you the last five steps. For detailed instructions, visit this article: Create, Modify, And Print Checks. 

Once done, I'd suggest running and customizing the 1099 Summary or Detail report. You'll be able to view all the payments to your 1099 vendors and their total amounts from there. I've attached a screenshot below on how the second report displays the check we've created. To complete this task, see the Total vendor payments reports section through this article: Customize Vendor Reports. 

I'm here anytime you have other concerns. Enjoy the rest of your day, @elisa7.