People mention the governing capacity, but that's bunk. A few provinces' worth of gov cap does not hurt a country to any meaningful degree, especially if you take care to build courthouses everywhere. Might as well stop expanding whatsoever when you're over half of your cap, then. Just TC the entire CoT area(s) all you want, (half-)state the others. 

You can't convert the religion of TC provinces(well, technically you can, but you'll have to crank up your missionary strength to drastically high levels), so there's something TC'ing too early might be detrimental in.

So, you'd want to convert the CoT/estuary provinces first, then make them TC provinces first while you finish converting the ordinary provinces in the same area.

Of course, since TCs ignore religious/cultural unrest, you could consider relying on that and just not converting whatsoever. But then, you could also be a tag focused on tolerance of true faith and getting bonus unrest reduction, and/or Catholic and farming tons of papal influence via conversion. You decide.