I'm going to be playing in Artificer soon and I plan to go the Armorer route so I've been reading up on the rules. I see that magic items can have Infusions placed on them so you can't double up by infusing an already magical item. The 'Arcane Armor' feature however doesn't have that restriction, as far as I can tell you could use any armor you can wear (magical or otherwise) as your Arcane Armor. The 'Armor Model' feature then modifies that armor, adding the abilities listed for the model you choose.

What happens then at level 9 when you get the 'Armor Modifications' feature? If the original armor was magical, you shouldn't be able to add infusions to it, right? But it also lists specific parts of the armor that can be infused, most of which would not be considered part of 'armor' under the traditional understanding (boots, helmet). I've never heard it suggested that you couldn't wear Boots of Speed (for example) because those would be included as part of your Adamantine Armor. So, if you had magical armor as your 'Arcane Armor', would you just be prohibited from Infusing the chest piece but you could still infuse the boots, helmet and weapon? I'm a little confused how this is supposed to work. 

You've basically got it right.

The most notable take away of the armor modifications feature is: you can infuse the weapon granted by armor model and can have 2 additional infusions, but only to the noted slots.

Also, incase you are confused, arcane armor does not count as magical unless it is infused or was magic armor before making it arcane armor.

Ok, that is good to know. I assume if you did have a magical helmet or boots those would get integrated into the armor as well but you wouldn't be able to infuse those either? 

I'm not sure how the rules work for integrating a magical helm or boots into the armor, if that's allowed, but you're correct that you wouldn't be able to infuse them since they're already magical.