Personally I wouldn't bother removing the air from the top of the bottles for 2 reasons.
1. CO2 is heavier than air and as such will protect your beer from the air (providing your not shaking the bottles up)
2. You want to create a large pressure build up in the bottle so the CO2 becomes absorbed in to the beer to give it fizz, you will lose that extra CO2 if it is merely sitting on top of the beer. (especially for a fizzy brew like lager or cider)
You will be able to determine how well the secondary ferment is doing just by squeezing to test the firmness of the plastic bottles.
I'd respectfully disagree here. First of all, there's going to be no shortage of CO2 - the gaseous CO2 in the headspace will represent only the tiniest proportion of the total amount of CO2 being produced. Secondly, the oxygen and CO2 won't just sit on top of the beer in nice convenient layers - they'll mix.
To be fair, the amount of oxygen in the headspace is not a massive concern when it comes to the risk of the beer spoiling, but I take the view that homebrewing is a random enough activity that it's probably worth making the effort to eliminate problems where possible, and squeezing all the air out of the bottle is such a straightforward activity that it seems silly not to.
And if you're
really concerned about a shortage of CO2, sling another few grains of sugar in. Yes, really: a few grains.
We usually measure the amount of CO2 dissolved in the beer as "volumes" - 1 volume being a litre of gaseous CO2 dissolved in a litre of beer. Typically, for fizzy lagers, you're looking at 2-3 volumes, so in a 2 litre PET, that's 4-6 litres of dissolved CO2 (I wouldn't want to open a 3 volume beer in an enclosed area, mind!!!).
The rule of thumb is that it takes 4g of sucrose to produce 1 volume of CO2. That space in the top of the bottle represents maybe 5cc, or 0.005 litres. So that space can be safely accommodated by the addition of a couple of crystals of sugar