@Ehayte

1. Yes, extended duration will be applied.
2. It varies depending on situation. Most of time I use Raging Strike > Apply Bio II, Miasma, Bio > Fester > Miasma II (If you close to enemy) > Contagion. This rotation will make your DoT hits harder with longer duration.
3. On my SMN, I tend to use Rouse+Spur when they're not on cooldown to maximize damage output from pets. Some are pretty situational, example is to use Garuda-Egi's Enkindle on large mob pulled or need slight burst damage (Example : Titan heart phase). Make sure Spur+Rouse is up to maximize Enkindle damage output.
4. You want to put Obey on your hotbar, as well Contagion so Garuda doesn't derp and use Contagion at wrong time. I made a macro for Contagion so I don't need to spam Contagion key in order to apply it to the enemy. You might want to experiment with your hotbar more so you feel comfortable to control your summons.