Creating custom page styles outside of page menu

I am trying very hard to wrap my head around the code structure of wordpress to create some custom post types for my site.

I have a premium theme, but the current design of it isnt the most efficient for my needs. I’ve also tried many plugins, which dont quite meet my needs either, so I am attempting to start from scratch. But I am a little confused on the files I need to create.

I have about a half dozen custom post types I am creating to handle galleries, products, affiliate links, ect. Only a few of those will be presented on the front end.

I am aware of the need to make files with either an archive(single, or content)-post-type. php

But i have a few questions regarding all that.

1. I read that it is often best to load CPT’s with a plugin. But if post types are normally defined in the functions.php file, how do i add my own to integrate with this?

2. I currently have my CPT’s and custom fields defined with the types plugin, and advanced custom fields. I’m not sure if i can pull the code from that to load it manually? Is there a reason why I should code these files manually opposed to the plugin?

3. My main problem with many plugins and theme structures is that it requires multiple steps to make one page, which I dont like. For example, my current theme has me uploading pictures in a photo album CPT, then having to go to the pages section and selecting a template to choose the album i just created. And then to display an archive of all albums I have to create yet another custom post type to display the albums in a gallery.

Is there a way to set template pages to the custom post type themselves. So all i have to do is upload images to the gallery, check off the appropriate taxonomies, define a parent album, and click post? This would speed up my upload process dramatically and wont require me to input the same data 2-3 times.

for example my galleries page will have two different templates assigned to it. one for clients, and one for non-portrait work. As the clients have additional taxonomies and options associated with it.

Thanks