Help, Guys! What is the best way to approach this set-up?

Dear Respected Warriors,

Can you help and guide me on the following:
I will endeavour to explain best i can in this issue:

I am in the making of a simple mini-site and just testing @the moment
and have hit a mental block...concerning My Download Thank You Page Delivery/Return
with a Payment Processor.

i have the cPanel Hosting and have putted to upload my 'Squeeze page' + Main Product Page,
associated image files, scripts and pieces into the Public HTML Folder
and initially tested this to all systems ok.

I am selling My products as a number of E-Books and corresponding Niche Video Tutorials.
These equal to a total of 50 individual files@ a total capacity of about 1.5GB.

Now The links to download all these files are embedded into my Download Thank You Page.
But i need to test download linkages on my hostings server side.

All the 50 files and Download Thank You page are saved in a
individual folder called "Customer Download" on my Desktop

Now my question to the Warrior Forum is that do i upload all the
50 files and Thank You page etc **individually** into my Public HTML Folder - Will that not
look messy and cluttered in the Public Folder? And potentially cause issues?

Or...

Do i just Upload the complete *Customer Download* folder as one complete entity into
my Public HTML Folder rather that individually on file by file basis? So it will be neatly sitting
alongside my Squeeze Page and Main Product Page.

So guys, which is the best and efficient way for the purposes of integrating
my Download Thank You Page with a Payment Processor which i will be setting up soon, such as, for,
e.g. Paypal, 2CO etc?

i would warmly welcome and appreciate your feedbacks.
Thanks so much.