What you did is the best way to do it, so don't worry!
The Phanteks PWM Hub is a useful accessory if you have too many fans for your mob's CHA_FAN headers. Even if you have only one or two too many fans, you can use simpler 4-pin fan Y-splitters rather than the Hub. The Hub has two major uses: MANY fans to connect to a few mobo ports, and trying to use 3-pin fans on a mobo that has only 4-pin CHA_FAN ports. (The Hub has a unique design that allows it to control both 3-pin and 4-pin fans from a PWM mobo header.) Neither of these applies to you.
The Phanteks recommendation about where to connect fans also does not really apply to you. It is based on a problem you appear not to have. There are SOME mobos that include fan headers with 4 pins but really are NOT true 4-pin headers operating in PWM Mode; they are actually 3-pin headers with a useless 4th pin. Now the Phanteks PWM Hub MUST have a valid PWM signal from the 4th pin of a true 4-pin header. If it is connected to one of these "fake" 4-pin headers it cannot do its job, and the likely result is that all the fans plugged into this Hub will operate at full speed all the time. To avoid the hassle and confusion of all that for users, Phanteks recommends that you skip the CHA_FAN ports and go directly to the CPU_FAN port because virtually every new mobo uses a proper 4-pin header for this function, so you're guaranteed to get a good PWM signal there. HOWEVER, this means the CPU cooler system then MUST be plugged in to the Hub on its white port (#1) AND it means that all the case ventilation fans are being guided by the temperature measurement inside the CPU chip, rather than by a different sensor in the mobo.
OP, since you did not need the Hub, connecting your fans to mobo CHA_FAN headers is the correct thing to do.
Billy ball bags, if all your case ventilation fans connected to the Hub are running full speed, the likely cause is that the Hub is not getting a PWM signal to use. This could be the result of three possibilities:
(a) the wires from the Hub that end in a female 4-pin fan connector are not plugged into a mobo 4-pin SYS_FAN or CHA_FAN header.
(b) They are plugged in, but that header is configured incorrectly in BIOS Setup. Check there. SOME mobos allow you to specify whether the mobo fan SYS_FAN or CHA_FAN header operates in PWM Mode (what you need) or in Voltage Control Mode (aka DC Mode). See if you have an option to change.
(c) The fan header you're using may have 4 pins but is NOT a true 4-pin header working in PWM Mode. In that case you only choice to achieve automatic control of your fans is to use Phanteks' recommendation. Plug the Hub's 4-pin fan connector into your mobos' CPU_FAN header so it can get a good PWM signal. Now make sure you plug your actual CPU cooler into the white Port #1 of the Hub. That is the ONLY Hub port that forwards a fan's speed signal back to the mobo for monitoring, and your mobo believes whatever that signal is, it comes from the CPU cooler. So make sure it does.
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