No, you don't have to. Once you configured and generated the first index table, it's done automatically. You can however turn this feature off, and also enable a wp_cron job under the Indexing & Cron panel.
Yes, by choosing the custom field under the General Options panel, the plugin will index it's contents - even fields, which are attached to a custom database table.
Try to lower the
Post limit per iteration option on the
Index table submenu, under the
Advanced Options panel. Try 10 first, and go lower if that doesn't work either.
Short answer, yes, you should. You definitely should if you:
Want to search shortcode content
Want to search tags, categories or any terms related to posts
Custom fields content
Have a big database of posts
You can index posts, pages and any custom post type (products, forums, topics, etc..) as well as attachments.