Straight away I'd advise not to bother with bait that far downriver. I've always found using bait that close to Fremantle tends to just attract the hords of blowfish. You might be better off trying small lures on some flats around East Freo or the Point Walter sandspit for whiting or slightly bigger lures for flathead. They should be there. I'm not much of an expert on what lures to use but lots of people on here are so hopefully they can point you in the right direction. I've found bait fishing is more worthwhile after dark as the blowies tend to slow down once the sun sets

 The ones with buckstail, Pt. Walter spit as mentioned above and don't stand still, cast up and down. Basically work as much of the spit as you can. Baits will get you maybe some trumpeter whiting if you can get through the blowies, but its hard to not get pissed off quickly. Bring a metal slice too, incase there are a few tailor around. Mulies on gangs slow retrieved works good too, although morning is generally slower biting i find. 

 I have caught a massive flathead in a crab net using red meat down there really close to the cliffs.