Using custom post types within a section of a template

Looping through posts

First of all, you need to have two separate loops – one for whatever it is that it’s displaying right now and second one for your custom post type. Right now the block where you want your custom posts to appear is located within the first loop, and that’s not good. I suggest that you read up on The Loop, and especially check some examples of multiple loops.

By the way, one can have nested loops, but that’s most likely not your case.

Templates

Also, from your comment not sure if that’s what you need, but for templating you can always take advantage of WordPress template hierarchy. That way you can have a separate template file for each of your custom post types, and then you fully control how each custom post appears.

For listing posts you need to look at the Custom Post Types display section.