Skimmer vacuum pumping waste through spa returns

I bought a vacuum to try and clean the dead algae etc from the bottom of the pool. I hooked the hose into the skimmer and started vacuuming. At one point I was losing suction because the pump basket was clogged with grass, etc., so I turned it off to clean the basket. When I turned the pump back on, I didn't have a good seal I think because I had lost my prime. I thought unhooking the vacuum hose would help, but when I did that, it dumped some dirty water into the skimmer. Once I got everything going again, I went to plug the vacuum hose back in, but I couldn't see, I plugged the hose into skimmer. When we started vacuuming again, it looked like all of the dirty water was coming out into the spa and filling it with the dirty water! What could possibly be happening? I would think that if I had a broken lateral I wouldn't be seeing the waste from the bottom of the pool, it would be somewhat filtered still, am I wrong? When I was vacuuming the first time, the spa did not get dirty. At one point I thought one of the pool returns was blowing out dirty water, but that was right where we were vacuuming, and none of the other ports were blowing out dirty water. I know there were two ports in the bottom of the skimmer, I initially plugged into the "back" one (per YouTube), but what happens if I ended up plugging into the front one? Thank you all for any help, this has been very disheartening :'(
 
So I may have figure this out? I found this in a very very old thread:

"Re: Why are there two holes at the bottom of my skimmer?
The second line from the skimmer in my pool is used for a supply to bring water from the pool to my second pump which feeds the optional jets in my swim out. Like a spa area. The second skimmer has it set up to feed my water fall which will have a seperate pump that can be turned on or off from a switch on my patio"

So if I'm thinking correctly, I must have plugged into the "front" port, so the waste was directly feeding into the spa?
 
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