Will the e-vehicle bills automatically sync with the government portal or do I need to upload them manually?How do I generate e-way bills in BUSY?

No.If you have enable feature of Automatic generation of E-Way Bill in then no need to generate manual from portal or upload on portal.You can follow some steps to generate E-Way bill from BUSY:
 Step 1: Go to Administration and then click on Configuration option.
 Step 2: Now click on Feature and option and then click on GST and VAT option 
 Step 3: Enable E- Way Bill Required option by specify yes and click on configure
 Step 4: Now specify From Place and pincode and enable other options as per 
 Required 
 Step 5: Now click on OK option and then click on GSP Configuration.
 Step 6: if you did not create GSP Yet then go to E-Way bill portal 
 Step 7: Login the E way Bill Portal and go to Home 
 Step 8: Click on Registration and then Click on GSP
 Step 9: After Click on GSP Registration Send the OTP 
 Step 10: Enter the OTP and verify the OTP
 Step 11: Click on Add New Option And select the GSP name and
 those are Webtel electrosoft PVT. LTD. And Pinnacle Finserv Advisors 
 Pvt. Ltd.
 Step 12: After Select One of the GSP'S Create User name and password and save.
 Step 13: After create GSP Go to Administration and then on Configuration and 
 Fearure and option and then click on GST VAT 
 Step 14: In GSP Configuration enter GSP ID's and then save the configuration. 
 Step 15: Now Go to administration and then click on configuration.
 Step 16: Now click on Voucher series configuration and select the sale voucher 
 type and then click on voucher series 
 Step 17: After click on voucher series click on voucher configuration and enable 
 Generate E-Way Bill after saving voucher and save the configuration 
 Step 18: Now Go to transaction and click on Sale voucher type and then click on 
 Add option.
 Step 19: Enter all the required details in their respective feilds in voucher
 for instance date. party name etc. and save the voucher and it will 
 show you the prompt for Genterate e way bill you need click on Yes.
 Stpe 20: Now you click on Automatic option and check possible error and rectify 
 them and then click on view and generate and check all details and You 
 can generate E- Way and then can print.