In a non-legacy Yahoo Store, there are two ways to add custom fields: through Catalog Manager under "Manage my Tables" and through the Store Editor, under "Types" (the Store Editor's "Types" are essentially the same as Catalog Manager's "Tables".) Whether you add custom fields from Catalog Manager or from the Store Editor does make a difference as each has its advantages as well as disadvantages.
To me the main advantages of using Catalog Manager to add custom fields are:
1) You can add multiple fields quicker
2) You can later change the field's name and even type
3) You can delete the field if you no longer need it.
4) All the fields that are available in Catalog Manager are included in the data.csv file if you download your catalog.
5) All the fields that are available in Catalog Manager are also included in the catalog.xml datafeed file, which is used by the comparison shopping engines, for example. (See the Search Engines settings in your Store Manager page.)
However, Catalog Manager has its limitations when it comes to custom fields.
1) There are certain field types that are considered to be "editor only". These are references, symbol, color, ids, font, objects, references, and orderable. Because these field types are editor only, any field with these field types is invisible to Catalog Manager, which means you cannot add a custom field using any of these fields types, nor can you access any field (from Catalog Manager) that has one of these types. Furthermore, since these types are not seen by Catalog Manager, if you download your catalog, none of these types of fields are in the downloaded CSV file.
2) There is a limit as to how many custom fields you can add, depending on what Merchant Solutions package you have subscribed to. In Merchant Starter, you can have a total of 50 fields in Catalog Manager. In Merchant Standard, you can have 80, and in Merchant Professional, 100.
Everything I listed as an advantage of Catalog Manager is a shortcoming of the Editor, and everything that's a limitation in Catalog Manager is an advantage of the Editor.
1) If you find yourself the need to add editor-only fields, your only option is the Store Editor's "Types".
2) Fields that you add in the Store Editor, unless you check the box that you want the field to be available in Catalog Manager, are not counted toward the maximum allowed custom fields limit.
3) You can exceed the maximum number of fields even if you check the box that you want your field to be available in Catalog Manager, however, if you do this, you will not be able to make changes to the existing fields in Catalog Manager until you delete the excess fields.
Which method you use is up to you and the particular task you are trying to solve with your custom field. If you are adding a field that you are sure you won't ever need to change or delete, you won't need it to be included in the downloaded data.csv file in Catalog Manager, or the catalog.xml datafeed file, use the Store Editor. If the field you are adding is an editor-only field, you have no choice but to use the Store Editor to add it. If on the other hand, you may at some point want to delete the field, or the field needs to be included in the download or in the catalog.xml file, use Catalog Manager to add it.