After you have created an account in eduappcenter and tied it to your institution, it is very easy to add custom configs by doing the following:
Go to admin menu in the top right of the page -> "Apps"
Select "Submit New App"
Make sure you set Availability to "Private" and set the Organization to your Canvas instance you tied eduappcenter to.
Complete the rest of the information and submit. You should now see the app under your Organization.
Finally, you need to make sure you whitelist it for your org. Do this by:
Go to admin menu in the top right of the page -> "Organizations"
Click on the name of the Organization you created the app in.
Towards the top middle of the page will be a link called "Manage Whitelist", click that.
Now you should see the app you created above in the "Our Apps" section. Make sure it is set to visible. (Note that the "privacy" field on this screen is for the LTI itself, not as part of the eduappcenter.)
That's it. It should now show in the app center within Canvas. This is a good way to customize existing pre-built LTI's, too. Let's say you like ACME LTI, but don't want a placement of it in the course nav, only in the content editor. You would blacklist the original ACME LTI in the eduappcenter and replace with your own copy of the original, removing the course nav placement in the xml.