If I understand you correctly, you want to save groups of indicators, so you can then later apply one or more groups to the charts, where as templates overwrite everything. Right?
As for colors, any saved indiators would not save colors. Those need to be auto assigned, so that they don't conflict with other indicators on the charts.
You can hide indicators without removing them either by right click option on the indicator legend, of if you go to Select Indicator screen, you can select multiple indicators on the right side, then right click on the selection and pick HIDE