one thing i always have to tell my female friends and clients... you will NOT get an overly muscular bodybuilding type physique by accident! It's damn hard work, and if it was easy I would be a LOT bigger and stronger!
So, to put on some healthy weight and muscle tone, just focus on getting plenty of protein in your diet, adequate carbs and healthy (unsaturated) fats - and start eating a bit more than you have done in the past.
Then hit the weights! Body weight exercises are fine but you can also use weights in the gym or at home for further results. I would suggest using rep ranges of 25, and 10 - 12 to target both Type 1 and Type 2 muscle fibres.
Some jogging is also good to help ensure you only put on lean muscle and not fat.