Hi Matt,
I am not familiar with "clean" or "dirty" prices? You just want to record the closing prices as percent of par, which is normally near 100 for a bond. We do have tips on recording bond transactions here:
http://fundmanagersoftware.com/help/bond_tips.htmlThe basic idea is that you keep your prices near 100 (percent of par), and the number of shares is the face value divided by 100, so the market value comes out correct. You shouldn't need to be changing prices between "clean/dirty" type of prices, they should always just be whatever the closing price was.
If you record your bonds as described above, then you can set the Income properties of your bond investments to "bond interest", and set the coupon rate, payment frequency, maturity date, etc. This bond interest information is used to calculate accrued interest. You can optionally choose whether or not to factor accrued interest into your yield (TWR/ROI) calculations. By default, it is included, but you can control this at "Options / General Preferences... / Yields / Include Accrued Interest in Yield Calculations". If you choose to not factor accrued interest into your yields, then none of those bond interest settings will have any impact on your yield calculations.