I saw that the Portuguese flag set was available in the British product line for Napoleonics. Would the British line infantry be the best to use for Portuguese infantry? Is that what is implied? Or should I go with Spanish troops? Any suggestions? I want to give Wellington some auxiliary Portuguese troops in his Peninsular Campaign I'm preparing.

From what I understand, the Portuguese uniform was similar to British. Earlier troops would however have the Belgic shako, later the stovepipe. For the Caccatore (sp?) use the flank company minis.

Yes, for this size of figure it is pretty much the same (IIRC the differences are in the lace or lack of it; the shoulder decoration and so on).   Some pictures here

As already pointed out, your best bet for Portuguese infantry is to use British. The only problem you will get is that the British infantry command strip comes with two standard bearers, because a British battalion carried two standards. The Portuguese battalion only carried one standard, which will leave a hole in your command strip which needs to be filled with an extra figure.

If the Portuguese NCOs carried a partizan or similar then cut  one of the standard poles down, or convert it to a sword or pistol.

I think I should be fine with two standard bearers. Most of the pictures I google seem to have two flags at the same time. One national and one company maybe? This one for example. I think that's Baccus even.

http://www.reinforcementsbypost.com/sites/default/files/image_gallery/P1120488.JPG

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A Portuguese regiment had 2 flags. The regiment at full strength would be split in to 2 battalion with one flag each. If the regiment was weak due to attrition or recruitment issues it would have 1 battalion and this would have 2 flags. I have 3 battalions of Portuguese. The 9th (2) and 21st (1) so the 21st has 2 flags.