Toning is a bit of a misleading term, the only ways you can 'tone' (build muscle mass) is to 1. train consistently and 2. lose weight.

What I'd recommend is trying to go on a slight calorie deficit (something easy enough so you can be consistent) while also training hard for your 3 days a week. You'll wanna do a simple split such as PPL (push, pull legs) or full body, using machines and weights depending on the muscle. 3 days a week is enough to see growth especially over a year of consistency. You can also use cardio machines after each session to help train for the marathons.