Since all major poker tracking tools (PT4, HM3, H3N, DH2 and much more) are missing features (the option to set a starting
bankroll or add additional deposits) you have to use additional tools. These trackers are good for studies off the table, or using the HUD.
Cheapest way to make good bankroll management is Google docs, other options are free available office suits with an Excel like tool.
There you can set up one table sheet per site/cardroom/Casino you play with data like day played, cash in, cash out and so on.
Another table may contain your bankroll management steps, like Stop/Loss limits, limits for moving up/down in stakes.
Next sheet can have currency conversions if you play with different currencies $, Bitcoin, and so on, these can be updated automatically und used for calculations to the own currency.
On addtional scheet you can make graphical views on your bankroll.
There are also tools available for free or paid that assist you in good bankroll management, not only in poker.