What is the best way to get user submissions into Wordpress while inserting items into custom fields?

You might want to use with Gravity forms with Custom Post Types http://wordpress.org/extend/plugins/gravity-forms-custom-post-types/ but definitely Gravity forms you can submit full posts and fields using Gravity. If you have classes of content you may not want appearing in your main blog index then consider a custom post type there are plugins that support this. Currently Gravity forms does not support Custom Post types on it's own but you can also register the user with the form submission and add them to a Mailchimp list etc. The Gravity forms add-ons are very useful. Custom fields can then be passed through those apis/forms extensions as well.