I am new to the whole tournament rating system and i am a first time TD with only one tournament under my belt but I have a question. Can any game between two rated player be tournament in as a rated game or does rated games have to fall within a tournament …
Match play is acceptable if the two players are within a certain rating range. Details are in the TD/Affiliate FAQs, which will quickly become your second stop (maybe even a Favorites link) on procedural questions 
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In general, matches are USCF ratable IF the players have established and published ratings within 400 points of each other. There are other limitations, such as how many ratings points someone can gain or lose as a result of match play.
The full match rules are available here:
main.uschess.org/docs/gov/report … atches.php
There are situations in tournaments which can justify exceptions to the match rules, such as an Under/1200 section which only has two players, or playoffs to determine the tournament champion. In such cases, the TD will need to contact the office and explain the circumstances which justify an exception to the match rules before the event can be submitted for rating.