1. Are you talking about setting the "Analyte Concentration" on all of your Replicates?
You can paste a list of numbers into the Document Grid.
You can also use the menu item "File > Import > Annotations" in order to import a .csv file with the values in it. The format of that csv file is a little tricky, but you can use the menu item "File > Export > Annotations" to see what that csv file should look like.
In Skyline-Daily, we added a feature called "Result File Rules" to automatically set the Analyte Concentration of a Replicate based on the Result File name. Here is a page that describes how to do that:
In addition to the Analyte Concentration on the Replicate, Skyline-Daily has also added an "Explicit Analyte Concentration" on the Molecule Result, in case your concentrations are different on different molecules, and they cannot be represented by the Analyte Concentration on the Replicate and the Concentration Multiplier on the Molecule. Are you asking about an efficient way to set the Explicit Analyte Concentration on your Molecule Results? I just noticed that it is not possible to import the Explicit Analyte Concentration using "File > Import > Annotations". I will look into fixing that in a future version of Skyline.
2. Skyline allows you to set the "Batch Name" on a Replicate if you need to have multiple calibration curves in a single Skyline document. A particular replicate will use the calibration curve composed of external standards in the same batch. I am not sure whether you will find that helpful with bracketed calibration. If not, can you explain more what Skyline would need to do?
3. If you want to average the Calculated Concentration values across multiple replicates, you should use the Pivot Editor.
Here is a page which shows how to use the Pivot Editor: