Software to help inventory set
I have had the same problem there are 2 ways you could do it.

Way One is to use rebrickable


Go to http://rebrickable.com/home Create an account.  
Then go MYREBRICKABLE and select My Sets.
Then click Add set to this set list and search for the set you want.
Now you can add all the sets you have.
IF you like you can go to the My Parts section and add any parts you
might have bought.
Now if you want to find out how many red 2 x 2 bricks you have you
can simply go to My Parts. Then tick the tick box where it says 'Set
Parts' and click update. All your parts from your MY Sets and My
Parts will now be shown below. You can see and example of this below.




Way two is to use  brickstock .


So what I do is open brick stock. 
Then Click Import and chose Bricklink Inventory.
Search for the set I want and then click ok. It
    then will create a file listing all the parts that make up the
set(You will see a small hard hat icon at the top right as it
download all the part images).
Do this for all your sets and combine the files and you will have
one master file.