You will have noticed some pages display different information about those two chakra. The updated information is that Mercury rules the middle chakra and Venus rules the throat. There are a few reasons for this.
Mercury rules communication and is the messenger of the Gods in mythology. This is similar to the function of the middle chakra that rules communication between the upper and lower chakra.
Venus rules self-expression which is ruled by the throat chakra.
Venus rules the thyroid, parathyroid gland and throat. Again also ruled by the throat chakra
Mars and Venus are a couple in mythology. Mars and Mercury certainly aren't.
The website is undergoing a huge update that will remove conflicting information.
Regarding the square, you shouldn't do any at this stage. You're clearly a beginner. Squares are intermediate and, in order to work properly, they need your chakra to be open and a permanent flow of energy to be established.
Try using aura magick instead. Appropriate colours are green (probably the best in your case), orange and yellow. Pick one colour and work with it. Don't try too many colours at once when you are beginner, or you'll just dilute the energies because you're most likely unable to handle them.
You can also do a chakra-related working, by vibrating the mantra of a chakra inside that chakra, and then programming the energies to achieve your goal. You can work both on your throat and middle chakra for this.
1. Breathe colourful energy into the specific chakra with the inhale;
2. Hold for as long as COMFORTABLE;
3. Vibrate the specific mantra on the exhale;
4. Repeat a few times, without overexerting yourself.
Do not get offended for me calling you a beginner. It's just a statement of fact, not meant in a demeaning way. Anyone past beginner level understands the answers to your original questions through direct spiritual experience.