The lines from the disconnect to the spa must be THHN/THWN individual conductors so that the ground is insulated. No 6/3 cable allowed. So it's back to the store for you any way.

The salesman was an idiot.
They always downplay the importance of doing it right because doing it right cost money. If you know this ahead of time you may not buy such an expensive spa or one with as many options, so they hold back the tidbit of info that wiring it can be expensive.

PLEASE contact an electrician first before buying anything else. Find out if they will even work this way with you.
If they will they can tell you what it is you need to know/get before you get it.

You were told so much crap. I disagree with Petey only in the fact that the HomeCenter expert doesn't care about price either. It's just blatant stupidity and the desire to sell what ever they have in stock.

First off, there's no restriction on how close your maintenance disconnect can be. That just has to be in sight of the person who is working on the spa equipment. The thing that has to be at least five feet away and in signt of the USERS of the spa, is the emergency pump stop. If this is a single family home, you're NOT required to have one of those.

The GFCI can be anywhere in the circuit (either in the main panel or at the disconnect), but it's almost always cheaper to put it in the custom little disconnect box they sell for spas.

There's so much involved to getting things RIGHT that use a large amount of electricity that you are going to stick you and your loved ones wet bodies into, if you are not familiar with the full Article 680 of the NEC, don't screw around. Get an electrician to do the whole thing. He's going to take one look at your cob job attempt to get up to the panel and either start over or go home at that point any how.

We are going to do such and such so all the electrician has to do is "plug it in". Not the kind of work we are interested in.

While not disagreeing with the advice above to get an electrician involved sooner rather than later, I'm not sure why anyone above assumed that the OP pulled cable rather than THWN. I'll be darned if I can glean that from the post.

Assuming that the wires in conduit are, in fact, individual THHN/THWN with insulated ground, if the conduit is large enough, it may be possible to splice them with a heat-shrink underground splicing kit made especially for this purpose. They run $20 or less at retail outlets.

But, please, get the electrician on board first. As if s/he didn't already have reasons for not wanting to work on a partially done job, knowing that there are wire splices wouldn't help, IMHO. And by no means should you do a simple splice with wire nuts and/or tape.

If it were me, I'd still favor unspliced wires even though it might cost more, but since you asked...

Here's the clue that it is 6/3 Romex: "25 feet of $2.50 wire".

Hah, your powers of deduction amaze me, Holmes. :-)

Perhaps I was fixated on the red herring:

I ran the 6 (3 wires plus ground) gauge copper wires myself.

Not sure the OP is still around so we may never know for sure, but I gotta admit that only Gucci designer strands insulated by real aligator hide is liable to cost $2.50/ft. per wire.

Cheers.