Yes, since Color Tools is not exactly a plugin, it is just an external application (and can be used not only with Sublime, but also with any other editor app), it is not possible to do some things. Currently, the Color Tools window can be called by selecting a color and pressing Ctrl+C+C or by selecting manually from the system tray. And you need to copy new color and paste it back to Sublime also manually (Ctrl+C in Color Tools, Ctrl+V in Sublime -- usually your color in Sublime already selected). Sure, this is not thorough integration (although still quite usable as for me).
I have started new color picker plugin
specially for Sublime Text, and I hope it will be finished as soon as possible. In that plugin, you do not need even to select a color anymore, you just move the caret and hit a shortcut, and it perfectly finds any color value under the cursor. Or you hit a shortcut to open the color picker window to generate a new color value.
But some ideas about "how it should be" still cannot be realized.
For example, I would like to add the command "Select color" to the autocompletion list when your cursor is in color (or when you edit, for example, CSS it should guess where a user may want to insert a new color value). But looks like it is not possible to execute custom commands from the autocompletion list.
P.S. New home of Color Tools is now here: http://indasoftware.com/colortools/