First, insert a blade into the blade holder. The tip of the blade should be protruding from the holder by very little. Your manual, if you read it, will tell you to allow the blade to protrude no more than just enough to cut through the thickness of the media you are cutting. For some overkill reason I have mine slightly more than that.
On the plotter display window push the "tool" button. The tool should read "CT1, CT2...up to CT5". The first number is the "speed". Mine is usually at 20. You can push the "Enter" button to move to the next number. That next number is the "pressure". Mine is currently at "60" for Oracal 651 intermediate vinyl. You increase or decrease the pressure by pushing the up or down buttons respectively. Press the "Enter" button again to the third and last "CT" number and that is the "offset". Mine is always at 30.
If you load some vinyl and get your display showing a "CT" tool number, you can make a sample cut by pressing the "Function" key 5 times, (you will see on the display that it says "Sample Cut"). Then press the "Enter" key twice. It will cut a rectangular box with the word "Cut" in it using a serif-type font. It should also cut that strip of vinyl off the cutter and it will fall to the floor if you don't catch it.
Take that sample and weed it. From that, make a determination if you need more or less pressure to facilitate easy weeding. You don't want to much impression into the backing paper if any.
I hope this helps.
I'm using Flexi 7.6.2 and don't have an issue with Flexi over-riding the plotter regarding the pressure setting. If your version is over-riding the plotter either find out how to set the pressure from Flexi or see if there's an option to turn that off.
Good Luck!