Features/Themes and Drush Make Files: How to manage updates? I am trying to automate my development by using Drush Make Files and Features. 

I am using Drush Make.me to create the make file.

I have created a Features module on my local machine. What's the best way of telling DrushMake.me about this module.

I guess I could upload it to my webspace and then put the URL into Drush Make. However, I am not sure if this is the best way of doing it. For example, what happens if I update the feature in the future. How will existing website that contain the old feature know that it has been updated.

Also I have my own custom Theme which I want to include in the makefile. If I just Zip and upload it, I would have to do this everytime I update the theme which doesn't seem very efficient (plus how will existing sites know that the theme has been updated).

At this stage, I would like to keep my theme and features private as I want to work out all the kinks.

Any advice on how to managed everything would be most appreciated.
You should build an installation profile to go with your make file.  Then, you could store your theme inside the installation profile.  There's a Drush command to make an installation profile; see this issue on drupal.org.  If you use this technique, you can just run drush pm-update to update modules, and then re-build your makefile and installation profile using the Drush generate-profile command.

Another option would be to just store your custom theme in a git repository.  You can load a module or theme from a Git repository.  See this answer for details on how to do that.