Saving custom meta fields using custom meta boxes and custom post types

I am developing a theme which makes extensive use of custom post types, custom meta boxes and within each meta box there are several custom meta fields.

I have a issue writing the function to save details for meta boxes that have several custom fields.If the meta box has only one custom meta field, it gets saved/updated. If the meta box has several, they don’t. I can’t use loops to generate meta boxes and display them because each one looks too different in the way custom fields contents are generated. So each callback/metabox display is unique.

Could someone point to me to a good guide to address a situation like this? All the tutorials I have found do not cover my specific case. I am just looking for a way to save/update all the custom fields in each different meta box for each custom post type. I would like to use nonce field while saving (already have a nonce in each metabox as hidden input).

Thanks for help!