Files can be saved in a number of different formats and this is no different for excel files. Of course the type of files that you use will be dependent on the needs that you have. CSV and XLS are two of the most common file extensions when it comes to spreadsheets. Here is a little bit of information about each one.
XLS
This is what is known as a binary file format and can hold large amounts of data that includes the actual data that has been input or imported from a PDF to Excel converter, the formatting of the spreadsheet and the formulas that have been included. If you have spent vast amounts of time transcribing data from PDFS why not look into How to make pdf into an excel and save yourself some time.
CSV
This is a plain text file and stands for Comma Separated Values. Each piece of data is saved with a comma in between. This file format is often used when importing information into various pieces of software from an excel spreadsheet or importing it into a spreadsheet. It is limited in that it does not save any formatting or formulas and can only work with small amounts of data.