When Skyline calculates the normalized area of a peptide or a protein, Skyline always uses your second formula there, and divides the sum of the endogenous areas by the sum of the heavy areas. This has the effect of giving greater weight to the more intense peptides.
If you do what you have in the first formula, you actually end up giving the same amount of weighting to the peptide with low signal as the peptide with high signal. There might be valid reasons to want to do that, but Skyline never does that.
Note that, for that first formula, you need to divide everything by two, because you are taking the average of those two ratios, not adding the ratios together.
Skyline will calculate the normalized peptide and protein areas using your second formula, so you do not need to do it yourself unless you are trying to verify that Skyline is getting the right answer.
In the Document Grid, there is a column called "Normalized Area" which will tell you the peptide's normalized area. There is also a column called "Protein Abundance" which will tell you the normalized area of the protein. (There is a binoculars button at the top of the Report Editor which can help you search for any column by name).
The normalization method that Skyline uses is whatever you have chosen at:
Settings > Peptide Settings > Quantification
If you would like to learn more about the Document Grid, this tutorial is helpful:
If you would like to learn more about using Skyline to compare abundances between groups of replicates, you should look at the Grouped Comparison tutorial: