I have an account that is mostly in a regular 401(k), but a portion is in a Roth 401(k). How do I tell the program that a portion of the account is in a Roth?

You can designate the portion of a 401(k) plan that is in a Roth 401(k) as seen in the screenshot [...]

I want to enter my 401(k) contribution as a percent of income. Where do I do that?

You can enter your contributions as a percentage of income or in [...]

Where do I change federal and state income tax rates and capital gains tax rates?

The program defaults to calculating federal income tax rates based on taxable income each year. But you can override this with your own average federal income tax rate. You must also enter your average state income tax rate. The program also calculates capital gains tax rates each year and assumes all capital gains tax rates are long-term rates. You can override this with your own rate as [...]

I have a lot of income securities. Many of these should be taxed as ordinary income (REITs), some are return on capital (MLPs), and others are regular qualified income. How best to model this?

You would want to create custom asset classes for these. Let's look at modeling a REIT as an example. Say that you project 80% of the future returns will be from the dividend, which is taxable at ordinary income tax rates. First, select your username at the top right and go to 'Account'. Then go to the 'Asset Class Assumptions' section. Look at the screenshot below. In this example I assigned an [...]

I have a financial advisor that charges a percentage fee. I also want to add fees for fund expenses. How do I do this?

You can add both fees to every investment as you see in the first screenshot below. This will apply a 1.25% annual fee to every investment account. You can also add fees by individual investment as you see in the second and third screenshots [...]