Making content and functions maintainable in the long run I've been playing around with drupal for a couple of weeks now and one subsisting doubt remains in my mind: what is the correct, 'Drupal' way to add your custom content? For basic text and links, a WYSIWYG editor that I've downloaded seems to be only about adequate (as it is a bit sluggish).

Because I want to extend website functionalities, like user input, I've been using .tpl.php files to modify content on specific nodes/blocks. For example, in some arbitrary file along the lines ofmytheme/templates/page--block--5.tpl.php there is code that prints to that page, like so

&lt;?php print render($page['content']); ?&gt;
&lt;div&gt;
&lt;?php my code here... ?&gt;
&lt;/div&gt;

But this isn't great for the future of this project as it's essentially hard-coding. Given that I will probably one day have several people uploading content or pass it on to a different admin, what's the right way to add more advanced features for maintainability?
I'm not quite sure what you mean. 

Block content can be held in the DB. .tpl.php files are as the name suggests used for templates. E.g. block.tpl.php is the template for all blocks.

If you have 2 distinct type of template for blocks then you could certainly create a block-alternate.tpl.php but there is certainly no need to create specific templates per block.

If you want to alter user input then add fields to your custom content types, or maybe look at the Webform module.