Would you want to only accept a deposit, or have an option of a deposit or the full amount?
You can accept payments for whatever you need, if you need to give the option you would want to create two versions of the Payment fields and then use some "Skip/Show/Hide" logic to only show one set based on the payment needs, if the user wants to pay in full you would display the set of payment fields that you connect to Paypal, and if they choose to only pay a deposit show the other set of Payment fields that you would not connect to Paypal but would just connect the "Deposit" field there (either a fixed amount or user entered amount).
This post describes a little more about creating payment options (different goal there but same method): http://forums.adobe.com/message/4399918#4399918
If you only want to accept a deposit that is easy, just don't connect the other Purchase fields to Paypal, only the one field for the deposit.
Thanks. Is there a way that I would be able to accept the deposit via PayPal?
Yes you can, I guess my answer wasn't clear.
You would have a field for the "Deposit", could be a fixed amount or a user entered amount, whichever you require and you would connect that field to Paypal on the Payments tab. Again, how you do this all depends on whether you want to give the option of full or partial, or if you just want to take a depost, no skip logic would be needed if you are only taking deposits, but if you want to give the option of full or deposit you would want to use the Show/Hide/Skip logic as described in the post I referenced, there is also this one with a few screen shots of the logic: http://forums.adobe.com/message/5922451#5922451