When recruiting - if you find the first location destination on flow chart and are using a 3 ops card - do you attempt to place all 3 cells there or do you place one cell there then move to next priority on chart?
3 Cells are placed in that first location you identified. See the Playbook, page #10, for an example; see also Rule 9.4.2.
2. What happens when you have higher ops on the card than the cells being used to say plot - (eg. 2 cells eligible to plot but you're using a 3 OP card) do you roll 3 dice and count the successes or are you only able to roll 2 as that's the amount of cells making the attempt??
2 Cells = 2 Plot operations; with the leftovers, you perform Radicalization. See the Example at the end of Rule 9.4.3.
If in one region there are 4 cells, 3 revealed and 1 hidden and I must plot with two - do I just use the ALREADY revealed cells as the cells that are attempting the plots? I was just wondering if you have to flip the hidden cell?
If you meant "Which Cells would the bot use?", then the answer is the Active ones (see Rule 9.3.1); if you meant "Which Cells should a human player use?", then the answer is whichever you want, but using the Active ones is a smarter move.