Genital warts are contagious, especially if you're having an outbreak, so it's always a good idea to communicate about and practice safer sex with your partner(s). The strains of human papillomavirus (HPV) that cause genital warts are distinct from strains that cause warts on other parts of the body, so you don't have to worry about getting warts on your hands or elsewhere.
Washing your hands thoroughly with soap and water after the deed is done and keeping the genitals clean and dry are also helpful. Or you can just avoid touching them if they're other places, such as your inner thigh or buttocks (you can make up for neglecting those other regions in the masturbatory repertoire, once the warts are gone). You can use a barrier such as a condom, dam, or non-microwaveable plastic wrap if the warts are on the shaft of the penis, the clitoris, or vulva. Transmission risk is greatest from contact with visible warts, so avoid touching them. However, there are precautions you can take so that you can continue to enjoy the myriad benefits of masturbation without worrying about warts. Like you suspect, when you have symptoms of genital warts, it's a good idea to be cautious in your diddling because it's possible to spread the warts from one part of your genitals to another. Woe's the day that anyone stops masturbating (assuming they want to masturbate)!!
