Do I have all annotations available from the start or do I have to format the .gedata file to include all annotations before I start?
No it is not necessary to have all annotations in the data frame (the .gedata file) at start. By selecting File and then Import in the program you will be provided several options on how to import variable and sample annotations. The program import .txt files. When importing an annotation file, the samples/variables in the annotation file will be matched with the samples/variables in the data frame using the annotation in the first column of the annotation file and the sample/variable ID annotation in the data frame. The ordering of the rows in the annotation file and the data frame does not matter.
After the annotations are imported and the original data file is saved the imported annotations will be added to the data frame (.gedata file). This can be a convenient way to build your data frame (.gedata file).