Transactional Replication Default Settings

We are using transactional replication in SQL 2008 for our data warehouse. Periodically, we need to add articles to one database or another and we have to re-initialize and generate a new snapshot. However, when the new articles are added, the default settings override the existing settings.

The two settings we need to persist are "Copy non-clustered indexes" for tables and "Copy permissions" for all other article types. Any help in changing the defaults for SSMS is greatly appreciated!