I am relatively new here, also.
For the first two weeks after registering, you get to be a PREMIUM member.
I dont have any special software that keeps track of my collection.
I just use a speadsheet (Excel)
I didnt find it to hard to enter my collections of HAVES.
You can enter your collection by dealing with each expansion deck separately.
Then the software here, will list the cards in that set. By pushing different buttons you can make the list alphabetical, or in numerical order (much easier for me).
Then its a few clicks to indicate that you have the card, and to enter in how many you have of that card.
After each page of 50 cards, you click the save button, and that is when I would add my notes about the newest batch of cards. (Unlimited vs 1st edition, error, etc)
No one expects a person to get all of their cards in within a day. But the two weeks of premium member ship was enough time for me to get me collection entered.
I think I entered in around 900 - 1000 cards in my HAVES list (Neopets and Pokemon combines).
If you want to get special software to help you get organized, then do what feels right.