There are two ways to add a discount or track deposits inside a project.

The first, and simplest, is to set this up as a custom line item with a negative price. To do this, simply add a new custom line item, and set the equipment price to a negative dollar amount.
This type of discount is useful if you want to discount to be applied to a specific room/system.

If you would prefer to apply the discount to the entire project, or use it in multiple projects, you can set this up as a negative Factor. To do this, create a new factor by going to Settings -> Company -> Factors. 

Then select '+Add Factor'.

A window will open where you can name the factor, assign a category and a description.
To define this factor as a discount, set the price to the desired discount as a negative value. Set the cost to zero, and click submit.

Once the factor has been created, go to the project's overview page and select 'Add Factor' under the Factors category.

A window will open where you can select which factor you wish to apply. In this case, select the discount factor you created. Then click 'Submit'.

Negative Factors and Line Items are also useful if your client has already paid a deposit and you would like that to be reflected in the project total. Choosing between the two is mostly a matter of preference.
Negative Line Items will appear in the specific room or system that the negative Line Item is added to, whereas the negative Factor would be applied to the whole project. You can create a negative Factor for your deposits, and change the value per project, as you add it. The process for both of these is the same as creating discounts.

Let us know if you have any further questions on this topic!