When you say you want to cross Port Phillip and Westernport, do you have specific start and end points you are thinking of?
StKilda to Sandringham ideally needs NNW but a due North works just fine. Tide doesn't matter on that run. Just be aware if it's low tide not to get too close to Green Point as the reef could trip you up.
If you are crossing the shipping channel on Port Phillip, just be aware that the channel is 250 metres across so line up a marker buoy and make sure there are no ships approaching from either direction. If you can see it coming even from a couple of kilometres away, then you should stop at the marker and wait for the ship to pass. The channel is (obviously) substantially deeper than the rest of the bay so you will suddenly experience very different conditions and you don't want to fall with a ship bearing down on you. You should also consult the shipping arrivals and departures website to know whether there are any ships due:
www.vicports.vic.gov.au/operations/Pages/ship-movements.aspx You will see ships out there - some may be anchored out on the bay waiting for their window to come in and dock. It's a bit unnerving as you try to work out whether they are moving or not. You look for smoke coming out of the funnels. Or if your eyesight is good enough, look for anchor chains.
Legally, you are not required to carry a flare on Port Phillip, but depending on your intended route across Westernport, you may require two different types of flares as well as an EPIRB, a compass and a waterproof torch. And of course, a PFD. There is no legal requirement for any other clothing but it is strongly recommended that you wear hi vis orange or yellow/green, and you consider water temperature and air temperature on the day - you don't want to overheat but you also need to be aware that if you lose your board and you are in the water for an extended time, it's the hypothermia that will kill you.
On right of way, a motorised boat has to give way to a human powered vessel (SUP) and has to slow down to 5 knots within 50 metres of any other vessel (including a SUP) unless it is involved in a race. But I wouldn't be aiming to press legal rights after you've been crushed by a merchant ship. When you see anything big and fast coming at you, you give way to them. Also, the bigger merchant ships in the channel have bugger all opportunity to turn to avoid you. The channel isn't wide enough. And the cost of one of them running aground is probably going to be greater than a compensation payout to your widow.