You can use the shortcut methods directly from the controller:
# Set
$self->cookie(foo => 'bar');
# Get
$self->cookie('foo');
http://mojolicio.us/perldoc/Mojolicious/Controller#cookie
However, if your intent is simply to store a value and retrieve it on subsequent requests, there's no need to set cookies directly. Mojolicious sessions use signed cookies by default, will handle the complexities of the cookies, and will verify that the values have not been changed by the client.
# Set
$self->session(foo => 'bar');
# Get
$self->session('foo');
http://mojolicio.us/perldoc/Mojolicious/Controller#session
If sessions are the best solution for you, make sure you set your app secret. Also, check out:
http://mojocasts.com/e4#Session