<<<I cant find a website I feel comfortable buying tickets to the colesseum, etc.>>>

You are in Rome for 2 weeks and there is no reason IMO to tie yourself to a specific day to visit the Colosseum/Roman Forum/Palatine Hill.
As things sometimes change weather, your schedule, strikes, etc.

If you want to visit the Colosseum on your own you can follow these directions to avoid any long lines.

But the directions and info is dated but it starts getting updated on Mar 8, 13 @ 04:28PM so read thru it.

Esp the different routes you can take from the Palatine Hill ticket entrance and you might as well start there and do the Palatine Hill 1st.
www.fodors.com/community/europe/rome-avoiding-the-long-colosseum-ticket-linequeue-palatine-hill-ticket-office-locations.cfm

But if you do wish to pre-book your ticket www.roninrome.com tells you how.

Also you might want to consider the 'Walks of Italy' tour that takes you to the off-limits underground (beneath the arena) and the 3rd level of the Colosseum, everyone here recommends it.

<<<is there any website I can purchase my train, bus tickets such as a C.I.S Ticket?>>>

No need too. Just walk into any Tabacchi (tobacco store which all sell metro/bus tickets (1 Day, 3 Day, 7 Day), phone cards, candy and other small items.

They are all over Rome and will have this type of sign http://tinyurl.com/aabr427

Also from newstand kiosks http://tinyurl.com/aou55fe

Don't worry about language problems you're a tourist the owner will know that you most likely want a metro/bus ticket.

In the tourist areas the owner will likely know some basic english like "1 metro bus ticket for 7 days".

If not, just hold up 1 finger, then say "metro bus' and then 7 fingers and they'll know you want one 7 day ticket .

Also roninrome.com has a section on how to buy tickets from a ticket machine that has an English option.

<<<Even the Catacombs!>>>

I don't think it's possible to pre-book the Catacombs?
The Catacombs are Church property and they run the tours, I've just never heard of anyone pre-booking tickets or even if that option is available?

But not a big deal, just show-up and at the ticket window and they will book you on the next available English tour.

Also roninrome.com has alot info and the bus routes to take there.

Also these dated directions are valid, a poster here used them 2.5yrs ago and Rick Steves still uses them in his 2013 guidebook.

But re-check the opening and closing times and days as those might have changed since that post was written.
www.fodors.com/community/europe/rome-catacomb-directions.cfm

Also look into the Scavi Tour (search here for info) which is an underground tour of the nercopolis and St. Peter's tomb beneath St. Peter's Basilica.

And look into the RomaPass, a 3 day pass which lets you bypass ticket lines at 2 of their listed sites plus 3 day of metro/bus/tram transportation.

No reason at all to buy before you go - except for Scavi tour and the Borghese. Otherwise easier and cheaper to get there when you know what you will want to do each day - you don;t want to be stuck with all outdoor stuff on a day it's pouring rain.

I third the above two comments.