Is there a guide, or if anyone has one, know where the best sectors you should go to for each of the commendation XPs? For example Science in Sirius and Sol sectors have been pretty awful (mission only reward 75-80 XP) but are pretty good for Diplomacy. etc.
For the most part, they're all equal - there's some variation in the random rolls each reset, but not consistently every reset. The main exceptions:
Trade: The Cardassian sector blocks are better for trade, because that's the only place you can trade for the gamma quadrant commodities, and also has assignments in almost every category that use those commodities.
Anything that takes GQ commodities as an input gets higher CXP because it's quite hard to accumulate them, which can also make Cardassian space just all around better for every category. Even recruitment is slightly better there than anywhere else except the personnel contacts at Starfleet Academy. Complete the consulate authority chains and special recruitment assignments become available around Cardassian space, and the Project Chrysalis chain unlocks some very good assignments in science and recruitment (additional volunteers has no inputs and gives over 400 base CXP. No actual reward doff/item, but still one of the few high payout recruitment assignments around).
Colonial: Any exploration cluster, except not out-of-the-box. You'll want to progress through the colonial chain in each sector. The higher you go, the more assignments you'll unlock, many of which give very good CXP (look for ones like Fortify Additional Colonies). Many of them are also split between colonial and another category, and those generally have a higher total CXP than single-category assignments.
Always make sure to check your department heads, too. They only cycle once every 20 hours, but they also get different assignments in different sectors. First Officer has diplomacy, Engineering Officer has engineering, Operations Officer has development, colonial, and sometimes recruitment, Science Officer has science and engineering, Medical Officer has medical and sometimes a development or two, Tactical and Security have military and espionage.
Also go through all the assignments and match up your duty officers. Like right now every day i get several critical success because i took the time to find the right doff for the missions and a lot of my engineer missions i get purple or blue items. Match up your DOFF's and try to do it with green blue and purple ones. In my case i got a purple DOFF which always gets a critical success on trading missions so im basically getting a 200% reward bonus on every completion. Spend the EC to find the exact DOFF's you need and continue running those missions.
The Cardassian sectors are also quite good for Diplomacy. You get a bunch of assignments like "Appraise Political Conditions on Cardassia", or "Moderate Cultural Conventions on Bajor" that only appear there, and many of them use officers other than Diplomats, which makes it easier to do lots of them at once.
There are also a number of useful assignment chains that only appear in Cardassian space. Two ("Project Chrysalis" and "Ghosts of the Jem'Hadar") both result in an unique purple duty officer, while the four "Consular Authority" chains when complete allow you to pick up assignments that let you trade an officer for a potentially much better one - those missions are also the only way to get rid of the bound guys you have bought from Lt. Ferra aside from just dismissing them.
For science assignments the sector usually isn't important. There are two kinds of science assignments that seem to generate a lot more xp than the others, and they appear anywhere. The first kind are the ones that require you to use the rare gamma quadrant commodities (which you can only get from Cardassian space). They are assignment chains and once you do one it will periodically come up again so you can do them over and over. The ones that use 4 and 8 commodities respectively give tons of XP, but the ones that require 15 and 20 commodities give you more dilithium. I get dilithium from other places so I mostly re-do the 4 and 8 ones (the 4 one is medical and the 8 is science). Make sure you check your science officer.
The other kind of assignment are the ones that require a rare duty officer trait. For them you need somebody with shroud (for "Genetic Sequence Jem'Hadar DNA") or telekinesis (for "Scientific Methodology Using Nonstandard Methods"). Jem'Hadar have shroud and Vorta have telekinesis. You can get them by doing the dominion story missions or by completing the colony chains in the Zenas Expanse and the Betreka Nebula, in Cardassian Space.
So overall if you are working on your duty officer stuff you should visit Cardassian space regularly.