There are several ways:
You can use the paint mode “Selection” along with the fill tool (paint bucket).
Or use the Stencil (recommended).
Just go here:
The stencil is used to have a selection based on color indices. If you only want to modify pixels having a certain color then invert the stencil (button with the orange rectangle at the bottom) and then right click on the color(s) you want to modify. You could also left click on them first (to protect them) and then use invert.
At the bottom you will find the check box “Auto update Stencil”. Disable it to not let the selection update once you placed other pixels.
If this option is enabled then you can even switch to another frame and will always have the selection updated accordingly.
The “typical” selection tools (magic wand…) and move/scale/rotate/transform/copy/paste are currently in the works.