Rogue Spear

I bought a 1987 MR2 earlier this year. Apart from a a clutch that went faulty after a month, it has ran great.
I dropped by a parts shops, to replace a blown headlight. While I was there, I decided to deal with some of the rust on the car. So I got rust treatment and some primer.
Having replaced the headlight, I started to work on one side of the car, I was horrified to find the level of rust. While I was sanding the car I discovered that someone had painted a lot of the rust, without first treating it and the paint was flaking off. Worse still, the rust was so bad near the exhaust and driver front wheel that simply sanding it opened up two small halls in the bodywork.
I knew this car suffered from rust, but never thought the neglect could be this bad. I have treated rust before on the small scale, but never on this scale.
The problem is, the car is going in for a service and MOT in a couple of days. I am just worried that the rust may have destroyed the underneath of the car and that it will be unrepairable.
Could anyone suggest a way to repair a small whole in the bodywork that does not involve replacing the exterior parts and being a newb with cars, is there a way to stop rust damaging the underneath bodywork. I really love this car, and plan to install a turbo when the existing nr engine goes.
Thanks in advance for any advice