Place a small plate in the refrigerator to chill; to be used later.
Place the peels, fruit and water in a large pot.
Add enough water to bring the total to 6 cups and bring to a strong simmer over medium–high heat.
Cook the citrus until the peels have begun to soften and turn translucent, and the liquid has reduced by about three-fourths; 40 to 50 minutes.
Add sugar and any add-ins and continue to cook, stirring occasionally at first, then more frequently as the marmalade cooks and the juices thicken.
Continue until most of the liquid has evaporated and the peels are totally softened and almost completely translucent; another 40 to 50 minutes.
As the marmalade cooks, the liquid reduces, the sugars thicken and the natural pectins activate.
You’ll notice the liquid go from a rapid, rolling boil with smaller bubbles to a slow, thick, tarlike boil with larger bubbles; this is the stage at which it’s most important to stir constantly along the bottom of the pot to prevent scorching and sticking; sugar is heavier than water and will concentrate at the bottom of the pot, making the fruit more likely to burn.
It’s also the stage at which splattering may occur, so take care in stirring.
When the marmalade reaches this point, add lemon juice and continue to cook, stirring constantly until the jam has returned to its previously thickened state; about another 5 minutes.
At this stage, the mixture should look thick and viscous with bits of the peel floating around.
The peels will never break into the liquid as with a jam; this is OK.
To test the marmalade's thickness, spoon a bit onto the chilled plate, return it to the refrigerator and chill for 2 minutes.
Drag your finger through it; it should hold its shape on either side without appearing watery or runny.
If it’s not there yet, cook it for a few more minutes.
Remove from heat and discard the vanilla bean, if used.
Divide among jars, leaving 1/4-inch of space at the top, and seal immediately.