Microscopic examination will allow visualization of the color in the crop or malpighian tubules. Keeping stocks pure is primarily dependent on conscientious attention to detail. Be very careful when making labels, transferring pupae and adults, putting eggdishes into cages etc. Particularly if your strains are not phenotypically defined, your methodology is the only way you will keep from contaminating stocks, and it may be impossible to determine that they are contaminated later. When possible, work with phenotypically marked stocks.
Recessive markers are better since contamination is easily remedied.
If you keep only a couple of stocks, separate tools can be kept for each. Eggs have sloshed onto the lid of a pan or cup and you use the same lid or cup for another stock without decontamination. This allows color-coding pans and cages without even writing the name. This can be quite time-saving. A free adult flies by and into a cage when you are blowing the mosquitoes back in.