I understand that periods always go inside quotes. However, would appreciate some feedback regarding the below situation I encounter often.

... and type "cd windows".

In the above example I'm telling users to type in a command. However, if I follow the traditional rules of keeping the period inside of the quotes I'd imagine that most users would assume they'd also have to type the period following windows. For this type of situation is it ok to keep the period outside of the quotes or should I continue with what I've been doing, which is using bold text instead of quotes?
I suggest that you borrow an appropriate typographical convention from a book. Try one of the many linux books. They sure have lots of command-lin-ery.

I can think of typesetting them using a good (not Microsoft's Courier New) monospaced font, on seperate lines (one command per line).

P.S.: Welcome to the Forums!
Thanks for the welcome and appreciate the reply. Unfortunately I've seen every imaginable way of doing this, which is why I thought I'd ask the forums at what they'd consider the best solution. In regards to Linux books they're and many of the man pages are using periods outside of the quotes.
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Well, I am pretty sure that typing commands in a monospaced font in separate paragraphs is the best option. And it is used in a majority of books. You can visit and see it first-hand.

... And my official MSDOS 3.3 manual uses the same convention.

What do you need that for? A printed book, a priter-ready PDF file, or maybe HTML or even Plain Text? What's your format?
Format is HTML.
Then you're free in your choice. HTML is quite flexible and you are not bound by typographical rules. I'd suggest not using quotes at all.

For short commands (say, up to 15 symbols) type them in-line, inside normal text, emphasizing with a monospaced font (or maybe bold monospaced or even color-highlighted monospaced) and being careful not to allow any line breaks inside commands (is it possible in HTML?).

As for longer commands, use the same font but write them on separate lines, and for very long ones — use several lines making line breaks in appropriate places.

And between command-lin-ery and surrounding text use vertical spaces of at least half the height of the font.
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computerhopeand type "cd windows".

... and type "cd windows". (BrE)

... and type "cd windows." (AmE)
Hi, Yoong!
What you have adduced are the correct rules of general punctuation. But I am afraid that's not how IT books are typeset, because that would make them less readable. You may yourself skim throw a couple of such books to get a notion.