Well you don't HAVE to CC as you go.. sometimes I do it sometimes I don't. KBS takes quite a while to dry.. probably as long as your enamels so CCing as you go will make the whole thing take quite a bit of time. Paint- any paint doesn't like smooth surfaces, it tends to peel off.
When you put tape down to mask off you are telling yourself that the paint is stuck down better than the tape.. the weaker one will always give way and it needs to be the tape.
I haven't used the blue masking tape.. its a painters tape and im not sure its perfect for the job once you have sprayed some enamel down.
A few things can help here.. you are using enamels so your colours are constant ( massive bonus) and don't vary once dry.. they do however take a long time to dry and do also like to peel like a single PVA sheet if not stuck down properly.
To help prevent this I find that Tamiya tape is the best.. not the wide 30mm stuff - that's extra tacky, but this stuff is brilliant..

http://www.ebay.com.au/itm/Tamiya-87033-87034-87035-6mm-10mm-18mm-Masking-Tape-Refill-Set-Paint-Tool-Spray-/111274448844?pt=AU_Toys_Hobbies_Model_Kits&hash=item19e87957cc

Because its enamel you can also add a little Penetrol.. helps your enamel stick down well.. can either wipe on the PF and allow to dry overnight, or my favourite way is to add some to your paint.
Can be bought in Bunnings etc..

http://www.paintaccess.com.au/products/flood-penetrol-paint-conditioner?gclid=CNrlwKu3wbwCFUUAvAodCSoAAg.

If you get a rough surface to your paint because you have sprayed very thinly or dryly, it collects dirt as you go and its very hard to get out again.. ive ended up repainting because of this.. when this happens you can CC - it seals the paint and if dust etc gets attached, it can be wiped off... idea is to make a smooth surface so less dust gets trapped... CC is very good for this.

But to get back to the original point, yes if you are going to partial CC then try to do it while the area is still masked.. your eye wont see CC to a line ( the black lines on the artwork).. it will see a light spray over another surface though as there will be a slight difference in the finish. But a rub back right at the start before any painting, a little Penetrol in the mix and the Tamiya tape.. you shouldn't run into any trouble at all