You can follow a similar approach for the selecting viewport as the ChSpace command. Issue the MSpace command, ask the user for some input (any input will do), then check if the CVport system variable > 1. Then simply run the vplayer command to set the relevant layer(s) overrides.
If you're setting the overrides through programming, then you simply need an entsel after ensuring the paperspace is current (cvport <= 1, use PSpace command to set). Then you'll need to look at the layer's xdictionaries and add a "ADSK_XREC_LAYER_COLOR_OVR" dictionary. This dictionary would then contain one of these for each VP in which it is overridden:(102 . "{ADSK_LYR_COLOR_OVERRIDE")
(335 . <Viewport's EName>)
(420 . -1023410173) ;RGB value of colour - e.g. this is green (color 3), -1023410175=Red(1), -1023409921=255, etc.
(102 . "}")