It is not that easy to find the endrega cocoons in Flotsam forests because they are not marked on the map. In order to summon the two Endrega Queens you must destroy all six of the cocoons which are located in two separate areas: the first group is southeast of the town, past the Nekker nests and north of a wrecked wagon; the second group is roughly halfway between the town wall and the ruined elven baths to the south, northeast of the burned down hospital.
Killing the queens can be insanely difficult at that point of the game. They are very susceptible to traps and bombs, so you can set up either or both devices all around the area, or cast Yrden to immobilize them and then hit them with strong attacks. Be sure to walk around the paralyzed Queen and attack her from behind as your attacks deal much more damage this way.
An Endrega queen often attacks opponents by charging which can only be avoided by dodging. Sometimes she also spits a toxic venom which is even more nasty, since it makes your Vitality drop very quickly. Waiting until after she has spit her venom before attacking gives you a bit of extra time.
Each Endrega queen patrols only a certain region. If you manage to get out of this zone, she will stop chasing you and go back to her lair (unseen to you). You can use this trick to recover and build your Vigor back up, throw knives at her back, or keep out of range and use Igni.
One useful trick which worked for me was to set 10 snares around the queen's area (or all of them in only one spot to trigger all at once and do massive damage) and then make her follow Geralt. Since a snare can deal 5 – 10% damage (at Alchemy skill level I), ten of them can do almost the 75% of damage to the beast, making the battle shorter and easier.
There is a third Endrega queen in the quest Lilies and Vipers added in the Enhanced Edition. If you go all the way to the shore line, and head back towards Loc Muinne there will be cocoons on the right. Destroy the three cocoons to spawn an Endrega Queen and four Endrega guards.