I found the best way to structure my "frankenblade" essays, similar to the way you have described, is to take it one idea at a time, and one text at a time. For example:
Paragraph 1:
The significance of nature and its role in the human experience is explored in Shelley's 'Frankenstein' through her use of....
Paragraph 2:
Alternatively, Scott uses his film BR to explore the effects of over-industrialisation and the destruction of the natural environment by...
(EDIT: Can I also suggest that, at the end of your second paragraph on whichever concept you're exploring, you make a strong value statement and draw out strong conclusions/comparisons. End it off such that you ensure you've integrated your ideas across the 2 paragraphs)
Then I would continue on to my next concept/point of comparison, looking at how it is expressed in each text by using separate paragraphs. I found that trying to refer to both texts in the one paragraph is messy, and often becomes quite convoluted and hard to follow.
How would you approach the nature aspect?
Just as you would any other theme or idea within the texts - you are to compare and contrast how differences in context affect the content of the texts, the values, and the ways they are expressed.
A difference in the ideas expressed by both texts is good - not all the ideas have to be concurrent within both texts. It is okay if you find they contradict one another, that's part of the comparison.
Some questions to ask yourself:
What techniques are used in each text to highlight the significance of nature to humanity/society?
How do these different portrayals reflect the social values of the time period in which they were composed?
Above all, remember to bring it back to "values and perspectives"