Do I need to configure E-Invoicing separately for each company database in BUSY?

Yes you need to configure e invoicing separately for each company database.
 For configure e invoice pelase follow provided steps
 Step 1: Go to Administration menu then click on Configuration option. 
 Step 2: Now click on Features and options then click on GST/VAT button.
 Step 3: Now Enable the E-Invoice required option and click on configure button.
 Step 4: Mention the From Place and pincode on then e-invoice configuration page.
 Step 5: Then enable or disable the next option according to your need and click 
 on ok button to save it.
 Step 6: Then click on GSP configuration and You will see options of enter Webtel
 and pinnacle ID'S.
 Step 7. Open E-Invoice Portal and click on registration option and enable 
 e-invoicing then Click on left side e-Waybill portal using your 
 existing credentials.
 Step 8. Go to Registration for GSP and Authenticate yourself with OTP then
 Add New user.
 Step 9. Choose GSP Name as Webtel Electrosoft Pvt Ltd or pinnacle finserv 
 advisors private limited then Enter the appropriate Username and 
 Password and add the user.
 Step 10. Enter the same username along with prefix and password in the 
 credentials table under GST/VAT GSP configuration in BUSY.
 Step 11. Go to Voucher series Configuration and select voucher type and it's 
 series in which you wants to generate E-Invoice.
 Step 12. On the Right side Click on voucher configuration and Enable Transport
 window and E-Invoice option on right side.
 Step 13. Now add voucher and it's saving time you will see the window,Do you 
 want to generate E-Invoice and then click on it.
 Step 14. You will see transport window fill it accordingly then select Automatic 
 and Check possible errors and resolve it accordingly.
 Step 15. Press F2 and save this window and generate E-Invoice and print E-Invoice.