Exirio automatically tracks your bonds, if you connect the institution where you hold them.
But you can also track them as manual instruments, within any Securities Portfolios.
For example, if you want to track the purchase at 98.15% of 40,000 usd worth of a bond (nominal value) with face value of 1,000 you will add the bond through the "Add Holding" button, and complete the Security form as shown below:
You should use the clean price to add the bond, account for the accrued interests you paid as an expense, and include transaction fees too - if any.
Assuming you bought the bond on 2 Jan 25 and a month later you received the coupon, your transactions will look as below:
Whenever you want to update the valuation of your bond, remember to use the clean price.