What options are there in BUSY to manage customers who order from my online store?How to create employee profiles and manage payroll in BUSY?

If your customer made an order from your online store, it will not sync directly into BUSY. You need to enter order in BUSY manualy from the transaction menu.
With BUSY Enterprise edition, you can configure Payroll and manage employee and their salaries. To configure this, follow these steps:
Step 1: Go to Administration and click on configuration. 
Step 2: Select Features / Options and click on Enterprises Features. 
Step 3: Here, you will a feature called Enable Payroll, set Y on that to turn it on.
Step 4: Click on configuration and can enable the salary mode(s) such as Monthly Salary, Daily Wages and Production as per the requirements.
Step 5: You can also configure for deductions such as TDS, Professional Tax, PF and ESI as needed and save.
Step 6: Next, you need to create employee from Masters under the Administration menu.
Step 7: Click on Add and enter all the necessary details such as Name, Group, Date of joining, etc.
Step 8: You have to set Salary structure and mention salary components such as Basic, HRA, PF, etc.
Step 9: For TDS deductions you need to click on TDS Details tab and need to mention deduction details and save.
Further you can go through our video and help documents for more clarification.