Peep and FiO2 will aid in oxygenation. If you have someone who is desatting or with a pO2 less than 60, you would increase one or both (need an order to increase PEEP). PEEP is great , but it may elicit higher peak pressures (pressures in the airway) and decrease venous return to the heart due to increased thoracic pressures (you may see a drop in their Bp)
Tidal volume and RR aid in minute ventilation, or CO2 removal. If you have a CO2 greater than the normal range, you would increase one to increase minute ventilation and thus, CO2 removal. (think about it, the more times you breathe per minute, the more CO2 you will blow off). Of course, you will want to look at your patient and see if they are over breathing the vent at all, otherwise increasing the rate may be pointless if they are already over breathing. Also, high tidal volumes may cause volutrauma, so you can only increase it so high. the exact opposite is true if the patient has a low CO2. You may also want to increase sedation in this case to keep the pt from over breathing and thus, blowing off too much CO2.
Sorry I don't have any references other than my brain which recently studied (and passed!) the CCRN.
That's the basics for manipulating the vent. When the patient is having metabolic abnormalities, it gets more complicated than I can describe and you have to ask yourself if they are metabolic or respiratory (side note, if you are in doubt in your practice, just call the doc or ask another RN or RT).
Overall, it sounds like you got a bad little education there. Refamiliarize yourself with the different forms of acidosis and alkalosis and know the normal ranges and go from there.