Hi Faizan,
" i could use f-58 to auto assign check number to payment document and after that i could use fchu to populate the assignment field with the check number assigned to that document right? "
Yes, that's correct.
" in auto payment program is all this process done automatically? i mean of check assignment from respective check lot and clearing bank item through auto bank statement? "
If you have the correct check printing program (eg RFFOUS_C) associated with payment method; and when posting payment in F110, you create the payment medium with corresponding variant, you should be creating checks (check lot should be populated in program variant).
After this, you should also run FCHU in order to populate assignment field with check number within payment documents.
When uploading EBS, if you use algorithm 011 then you don't need to populate assigment field and when importing EBS (with proper configs.) you can clear gl bank line item directly with check number (no need to use FCHU).
Best regards!