it is not easy to do this calculation precisely, but with the Pareto Rule (80/20) you can come a long way.
Firstly, CO2 can come from a number of sources, among which for example the footprint that is related with the products and raw materials that are coming into the company. Another emission source is that there are other greenhouse gases (beyond CO2) that might be related to the activity of the company, which should be calculated with its specific multiplication factor. Maybe it is a product that decays or a chemical transformation that produced one of the six official greenhouse gases or you work with refrigeration gases.
Finally (third) there is the energy consumption of the company (electricity, fuel, ...) that can be converted in a CO2 amount. For example in Italy, I remember that 1 kWh of grid electricity comes from (national average) 2.6 kWh of primary (fuel) energy, so you need to find the CO2 emission number of that fuel mix in the power plants for your calculation. Also miles, driven for the company's activity, must be included in the energy related CO2 emissions. There may be still other energy uses.
My suggestion would be to start with the energy consumption (this is my area, where I feel most at ease). In that way, group all energy streams that are similar and find the total amount for each of them. It might be gallons for transport, cubic feet for natural gas and kWh for electrical energy. Then you find the multiplication factor (the amount of CO2 for each unit of these energy streams) and multiply. The sum of all the multiplications is the CO2 emission equivalent for the energy consumption.
Please tell me if this helps you.