Agreed: first go over your tek (post it) repeatedly until you are actually completely clear not only how but also why you do everything mentioned in it. Otherwise if you try to follow a 'recipe' without the skill and understanding it is very easy to make a mistake but what's worse: not notice it nor understand what you should do.
Maybe walk us through the tek you want to use, prove to yourself which parts you get and learn the parts you don't get, we can point you towards the chemistry you need to study...
Answer to your question, not to be a dick about helping you or not: you don't make the lye in the sep funnel. The funnel is purely for separation of the phases / layers, the liquids floating on one another like oil on water. Before you're ready to do that you need to make the lye in another container of the proper material like glass, preferably borosilicate. Dissolving lye in water heats it up so it must be done gradually and with care or it could locally get too hot, you don't want to do any of that in the funnel. Also you use that lye solution to basify your strained and pooled bark brew to a certain pH you check with pH paper (or a pH meter), again it is inconvenient to do this in the funnel.
Only after all that do you put your solution in the funnel with a non-polar solvent to extract. I would hope that the tek is clear on the sequence of steps. You don't just throw everything together. What each step accompishes but also the tricky aspects like lye heating up explains why it cannot or should not be done differently.
