If you cook the bone stock the night before, you will see a solid fat layer floating upon open the stockpot/pressure cooker lid, sweet, remove all of those. If not, place the whole pot/cooker in fridge or something to cool down for 10 minutes so that all the fat and impurity could be solidify and easily to be remove.
Strain everything solid in there (if you were using pressure cooker, just pour it over a strainer into the stockpot). Pick out the bones and your secret weapon (if used) and let them back into the stockpot with clean&clear beef stock. Discard everything else.
Bring the stocking liquid to boil level, then adjust heat to simmering (keep this simmering until serve actually). Now go ahead and season this Pho broth by adding fish sauce(if only good fish sauce, otherwise use salt), rock sugar (if needed), or seasoning powder(msg free mushroom seasoning powder, bouillon, or even msg, etc depend on your situation). Taste it a little overpower then you normally would, cause when serving with rice noodle and raw veggies, it will be balance out.
Prepare and add the spice bag into stockpot. Set the timer or note somewhere to remove this spice bag from the broth after 1 hour or when your could hear the Pho fragrant coming out of the cooking broth.
(optional) Now, if you're using brisket, tender, flank, tendon, etc.. any cooked meat as toppings, go ahead and prime them by soaking and blanching just like the bones, you could skip the roasting though.
Add all the prime meats & tendon to the cooking stock when it's boil then adjust to simmering. Most people would afraid to replace cover; but if you did well with priming all bones/meat and assuring the heat is at low, then go ahead and close the lid to preserve aroma and water level.
If you have pressure cooker, then instead of the above, fill your cooker with enough water to cook the meats/tendon, and just pressure cook them on the side.
Prepare an icy cold cooked water bath. Upon remove meats (about 1 hour), tendon (about 90 minutes) from the stockpot, submerge them completely in cold bath. If you're using pressure cooker, reduce the time and strained the remaining juicy water(use to cook meats) into your stockpot. When all cooked meats and tendon are cool to the touch subsequently, remove them from the water bath.
Check back on the broth to make sure it taste, add more water if needed and re-seasoning it too. If you think the spice is not present, go ahead and add back the spice bag, but don't forget to remove when the aroma come up or the broth will be overwhelmed.