Select the custom shapes tool from the tools and then select the layer option. Select a shape from the presets picker and apply to the current art board.
You can also set a color for the design say red or green. Apply another vector design or the same vector design with a different color. Go to the layers panel which can be found in the window menu and set the mode to darken or lighten etc. This really only matters if you are on top or partially on top of another design. Also sometimes there will be no change as you are applying something like a lighter color on an already light color or trying darken with a black object.
You can also use the presets with the edit menu and fade command. Apply the preset and then use the fade to change the opacity and mode. Select the custom shape tool in toolbar and select a preset from the picker (control bar). Select color and select 'pixel' as pick tool mode and then apply the tool. Goto the edit menu and select the fade command. Change the mode and change the opacity and click OK. As soon as you apply another effect or add a gradient or adjustment, you will lose the ability to fade - it is only the last action.
Go to the top left and select the pixel mode and then set a mode (found in the control bar at the top) such as darken etc for the current selected preset or use a rectangle etc. You can then apply it over and over, though the only way to correct it is to use the undo or history panel. You can also use the fade command found in the edit menu and that will enable you to correct the last used (darken, linear, color burn etc) as well as change the opacity. You can also do the same on new layers but then you will have to use the layers panel to change the darken / difference etc and opacity and not the control bar.
There are many different modes available : Normal, dissolve, darken, multiply, color burn, linear burn, darker color, lighten, screen, color dodge, linear dodge (add), lighter color, overlay, soft light, hard light, vivid light, linear light, pin light, hard mix, difference, exclusion, subtract, divide, hue, saturation, color and luminosity. There are a few others such as clear and behind etc that appear depending on the circumstances. Note that if you are in 32bit mode etc some of them are not available and will be disabled.
Strokes can also be used with darken / difference / lighten etc. You can have a design with no fill and a stroke and that will also blend, depending on the stroke color, with the underlying layers. You can create all kinds of truly weird and wonderful line designs by using the stroke only designs.