First, do your research! Then, figure out how much you want to put into it! Stick to it....
And for the unskilled the best rule is buy it already restored... Most cars (outside of a really good deal or a really rare car with an inflated price) cost more to restore than buy outright. But that's not your question...
On the whole my rule of thumb is I don't want to have to do more than a 40% restoration overall.
The frame and the drivetrain are the "bones and heart" of a car. If they look bad, walk away. Unless you just happen to have a drivetrain in your garage that you are dying to put into something, but that means a low ball offer.
And then, yes, start adding up the body and interior parts and subtract that from the buying price if it is over priced according to your research.
I've got a buddy who takes half the price of needed parts and adds that in for his time. He clearly states his "deductions" describing the work needed. Most of the time he does get the car for his price... and he buys several each year. And he describes the cars he didn't get as "Well, I've been laughed at before...."
Unless you have access to a paint booth or want a rat rod, you need to know paint prices I know that's not a part of the negotiating on a rusty car, but it is still an out of pocket issue. If you spend more than 40% repairing and replacing rusted stuff, then you are likely to wind up "under water" on the car....
Of course, if I ever find a 61 Impala like I drove in high school, I'd probably pay three times what it is worth even if it is a pile of rust. I'll hold it together with a metallic paint job!