Meteor was designed so you structure your app pretty much any way you want to. So if you don't like your structure, you can just move a file to a new directory, or even split one file into many pieces, and to Meteor its pretty much all the same. Just note the special treatment of client, server, and public directories as specified in the main documentation page: http://docs.meteor.com/.
Just lumping everything together in one HTML fill will certainly not emerge as a best practice.
Here's an example of one possible structure: in one of my apps, a discussion forum, I organize by module or "page type" (home, forum, topic, comment), putting .css, .html, and .js file for each page type together in one directory. I also have a "base" module, which contains common .css and .js code and the master template, which uses {{renderPage}} to render one of the other modules depending on the router.
my_app/
lib/
router.js
client/
base/
base.html
base.js
base.css
home/
home.html
home.js
home.css
forum/
forum.html
forum.js
forum.css
topic/
topic.html
topic.js
topic.css
comment/
comment.html
comment.js
comment.css
You could also organize by function
my_app/
lib/
router.js
templates/
base.html
home.html
forum.html
topic.html
comment.html
js/
base.js
home.js
forum.js
topic.js
comment.js
css/
base.css
home.css
forum.css
topic.css
comment.css
I hope some more specific best practice structures and naming conventions do emerge though.
