Tell link_to explicitly what route to use?

Sure. Use name routes.. so rather than use something like:

map.connect 'example/:action', :controller => 'example'

use:

map.example 'example/:action', :controller => 'example'

this way, you can use example_url(:action => 'whatever') to create
the url for that route.

Hope this helps,
Damien

Sorry if i'm not following, but you can use the named route in the
link_to:

<%= link_to "Some link", my_custom_route_url(:action => 'my_action') %>