Amending via e-file:
E-file is only available to amend forms 990, 1065, 1120, and 1120S.
For Form 990, open the same return you had already e-filed and was ACCEPTED by the IRS. On the Information page, check the box for Amended Return. Click on NEXT and E-file your return again - there will a charge.

For Form 1065, open the same return you had already e-filed and was ACCEPTED by the IRS. On the Information page, check the box for Amended Return and fill out the Amended Return Statement. Click on NEXT and E-file your return again - there will a charge.

For Form 1120 you can file an Amended Return or a Superseded Return.
Just open the same file that was already ACCEPTED by the IRS, check the box for Amended or Superseded. Form Amended returns, also fill out Form 1120X. Click on NEXT and E-file your return again - there will be a charge.

For Form 1120S you can file an Amended Return or a Superseded Return.
Just open the same file that was already ACCEPTED by the IRS, check the box for Amended or Superseded. Then fill out the required Schedule for Amended or Superseded returns. Click on NEXT and E-file your return again - there will be a charge.

Amending via regular mail:
Any type of tax return can be amended by mail. Just modify the same return that was accepted, print it and mail to the IRS.
Forms 1041, 1065, 1120, and 1120S offer the option to check the Amended box and print it on the return, so it shows it is Amended.

Form 1040 does not have an Amended Check box available, but just printing and mailing a regular 1040 tax return to the IRS after your return was already accepted via electronic filing or paper, will take care of the problem. To make sure, attach a cover letter explaining that it is an Amended return.