The features that won't be working are the scheduling part and StealthPatrol which are the ones that you won't be using anyway right ? So no big deal.
Yes the SMARTPlacement will take a long time to finish the first time you run it, it will get faster with time don't worry. For the boot defrag you need to tick the little box from my screenshot and restart the pc. It will do the defraging just before the pc enters windows. The boot time defrag takes care of those files that have been locked by the OS and cannot be defraged while in windows(like pagefile, hibernation file, ntfs metadata etc.). So yes i would advise you to do this aswell, it shouldn't take that long though.
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Space management has more than one feature and i would advise you to read the documentation for more info on how to use it. Infact PD's documentation is very well written and quite an informative read. Their blog is also a great source of info. If you have any more questions about the product please read the documentation first before asking here, everything is very well explained and with the risk of sounding rude, everything you are asking here you could learn from PD's documentation. If you can't find the info that you want then you can also ask their customer service since you are now their customer aren't you ? So use the support that you payed for. Good luck with using PD, i have a feeling you are going to like the product.