I am having trouble understanding how depreciation was calculated in my books. Can you explain how it was done?

For knowing how depreciation was calculated in your books.You have to know how 
Depreciation has been charged in BUSY. Below are the steps to know it.
To define the depreciation rate, please follow the below steps:
Step 1: Go to the Administration menu.
Step 2: Click on Master and then click on the Modify option. Search for the Fixed Asset 
account in which you want to charge depreciation.
Step 3: Once you have found the account, open the Fixed Asset master in modification 
mode.
Step 4: Click on the Account group and a "Rate of Depreciation for the account" window 
will appear. Define the depreciation rate here and then save the master.
For passing Depreciation entry below are steps to follow:-
Step 1: Go to the Display menu and click on the Depreciation chart option. Then click on
Income tax.
Step 2: Define the Depreciation account and click on the "Ok" button.
Step 3: If you want to pass a depreciation entry for all accounts in one go, press F4. 
A window of "Generate Depreciation account" will appear. Click on the "All accounts" 
option and then click on the "Ok" button.
Step 4: If you want to charge depreciation of only a single fixed asset master, keep the 
cursor on that account in the same report as it'll highlight in blue color then press F4. 
A window of "Generate Depreciation account" will appear. Click on the "Selected account"
option and then click on the "Ok" button.
This way, Depreciation entry will be passed accordingly for fixed asset accounts.