Edit (patch) a binary file in IDA Pro
I think IDA used to have a feature to do that, but it's not present in the current versions.
You should just use a hex editor. Note the file offset in IDA and edit the file at that address. If you'd like to see the changes in IDA, use the "File" -> "Load file" -> "Reload the input file" menu item.
IDA 6.2 has the "Edit" -> "Patch program" menu enabled out of the box. No need to modify idagui.cfg. There is also an "Apply patches to input file" option that that will modify the target file.
Possibly edit:
idagui.cfg: DISPLAY_PATCH_SUBMENU = YES
If the menu is not enabled, then use
Edit/Patch code/Change Byte
select the instruction you need to change in "IDA View" subview.
switch to "Hex View" subview. You will see several highlighting hex numbers.
press "F2", edit it, when you finish, press "F2" again.
That's all. you will see your change in other subviews.