why is this not "with which pot?" . I said "b'toch eizeh sir" - why is that incorrect?
I agree. In Hebrew we say באיזה סיר and it can mean both: "in which pot?" or "with (or using) which pot?" and we can say בתוך איזה סיר? to mean "inside which pot"? so I think it should be accepted.
Could you say "?איזה סיר" meaning "which pot" or do you have to have the "ב" to be correct Hebrew?
Yes. When you say איזה סיר it means just "which pot".
Kedera is also a pot