Employer E-Sewa is a initiative by EPFO in which
Employers are requested to Register their establishments and create their user id and password through this portal.
After registration employers can upload the Electronic Return and the uploaded return data will be displayed through a digitally signed copy in PDF format.
Once approved by the employer online Challan will be popped based on uploaded return.
The employer may choose to make the payment through internet banking of SBI or take a print out of the Challan and pay at any designated branch of State Bank of India (SBI).
So, after that no need to submit different kind of forms such monthly (12-A, 5-10 etc.) & annual (3-A, 6-A).
on other hand E-Return Tool (Version 4) is to help you to prepare above ECR Format, it's just like a software provide by EPFO to maintain & Generate data's for contribution towards EPFO.
Hope this will clear your doubts.