If you're worried about all your drilled holes lining up, then you're probably not securing your pieces well.
I don't know what materials you're working with for the base, but you can probably use a couple of wood screws to temporarily secure the top to the base. (I'd say clamp it up, but this would be tricky to clamp.)
Once you confirm position and alignment of the top as screwed onto the base, drill all the bolt holes straight through; they're now guaranteed to line up. (Obviously, don't put your temporary screws in the spots where you plan to run your bolts!)
Then set your T-nuts from the top - if you want to countersink they'll be certain to be flush, else if you're working with a soft plywood, you can probably just pound them flat with the hammer, plus the bolts will pull them tight from below. You want to set them with a hammer even if you've countersunk, because you want the flanges to dig into the wood so the nuts can't spin. You'll also have to make sure the bolts are the right length, or the tip may project up through the table. (To make minor adjustments, just add more washers underneath.) You can remove the wood screws now... and easily unbolt the the base and secure it again any time you need to, even after finishing the top with padding and felt.