Hi
I am not one of the main guys but will try to help where I can
Firstly, can you name the iso that you have running or used to install please ?
For example, TinyCore-current.iso
2) There is a wiki that might answer some of your queries and I think you may be looking for this one?
http://wiki.tinycorelinux.net/wiki:install_apps3) But lets take your clockywock as an example.
You choose to download, install it as onboot or ondemand etc
---You chose ondemand.....there are some options better suited to users with certain types of persistence but lets not get too far ahead.
Once the APPS control panel, called Apps browser gives you a signal that its downloaded with the yellow background and OK message
Then click anywhere on empty desktop, is one way of accessing the menu (there are other ways but I assume you come from MS land) and choose the "ondemand" then click on your clockywock
Now you can click on the terminal icon in the wbar panel and run the command clockywock
------------
If parts of the wiki don't make sense, let us know as a wiki is only as good as the message received
-------
apps audit
Now to maintain, meaning to swap your tcz(s) from onboot to ondemand and vice versa then
click on apps browser
pulldown and select maintenance then do things
----Pretend you love clockywock so much you want it onboot
go to ondemand maintenance first and delete it from the list
(You are not deleting the file just a list item)
then click onboot mantenance item and scroll down to clockywock and click the ADD button
PS where did you read about apps audit please, the term may be out-of-date....not saying it is but I would like to check it
see image for better explanation