Use in External Forms
Form Tools differentiates between internal and external forms. You can read more about the distinction here, but internal forms are forms that are created and exist within Form Tools only; External forms are forms that you've created yourself and submit their data to Form Tools.
The field types that you create and customize via the Custom Fields modules are automatically available for use in your internal forms. You just pick the new field type on the Edit Form -> Fields tab and you'll see it right away in your form. But what about External forms? How do you see them there?
The answer is that it all depends on the extent and nature of your field type. The most important part is that data from your external form needs to store the data in the database in a format that the field type can understand.
A little context
Form Tools was originally designed to be integrated with any web form, regardless of how it was created. This is very powerful. However, as time went on and the interface improved, the gap widened between people's forms and what Form Tools could offer. Version 2.1.0 of the Core was deliberately designed to allow the extension of the field types, even though this would mean actually adding those fields to your external forms required additional work. The ultimate goal is to have Form Tools handle all aspects of form management: including the form creation. We have a Form Builder module currently in development, to be released later this year. That module will allow you to use any of your field types created through this module (or any others!) in forms published directly on your site. Because the markup and code generated for your forms will be pulled directly from the Form Tools database, no additional configuration will be required.
So, to sum up: if you wish to re-create the form field types you create within this module for use on your site, you'll need to do it manually. This may be quite a bit of work, depending on exactly what you're doing.