The gist is just an example, you'll need to modify to fit in with your theme (in general the default page templates may not work with your theme - and so likewise need editing).
> For the plugin to work with my theme, I had to uncheck, What do I do in this situation if I am using the page as a custom template?
If you created a page template using the gist, and then created a page and selected it as the page's template then WordPress will use that template for that page regardless of whether you've checked/unchecked that option. The gist examples operates completely outside the Event Organiser, and simply uses the functions it provides.
Regarding the height/width of the venue map. There is a bug with
eo_get_venue_map() in 1.5.7. 'Normally' (and in 1.6 you will be able to) you can pass attributes as a second parameter:
echo eo_get_venue_map( eo_get_venue(), array('height'=>'50px','width'=>'50px');
1.6 will be out a few days after WP3.5 is released - which is being released Monday.