2) When I get Tms/Hms, is there a special menu for them? If so, I need directions.
Not exactly, usually TMs/HMs are marked with a little disk thingie in front of the item, and what differentiates HMs from TMs is the fact that HMs come up in red letters when you attempt to sell them.
3) On the mission that you go to a cave and find Tyrouge, an Item is requested. Where/how can I get that Item?
Usually the item is something that you already have in your inventory/bank or you might have to buy it. The game isn’t likely to just ask for something that takes a long time to find. What you can do is read the green letters, write it down and go through your stuff to see if you have it, and then take it with you on the mission.
4) What are the bean-like objects in dungeons for?
Food, I believe.
Ones I’m not so sure about.
5) What are the orbs for?
7) When you go to the third option of the menu, then select your main, then the third option....what is that?
6)How do you use items on your partners?
Hit B to open up menu, go to the second option (dogu), select an item that you can use on your partner, and choose the second option (watasu).
Q: I beat the Zapdos dungeon, and the one with the Xatu, but now I'm stuck doing missions from the old dungeons. When/How do I unlock a new location?
A: Try going around town and talking to people to unlock events. Mainly people in town square, and also Whiscash.
Q: Would anyone be able to provide some information on roughly what level my pokémon pair should be at before I run off to encounter any of the bosses I'll have to battle? I'd much rather know if my creatures are capable of taking the opponent down instead of fining out the hard way and having to train endlessly~
Anythng past Zapdos would be much appreciated
A: Usually around 20 or would be good for the dungeons after Zapdos, although you can probably manage with around 15 if you have lots of healing items and PP recovers along with fused attacks. Training at Makuhita’s place really helps, and you’ll want to pick an area that you can quickly go through while still getting lots of exp. For example, if you have Charmander then go train in the forest areas and if you have Totodile, then you should train in the lava dungeons.
Q: I'm in the process of beating the 3rd dungeon. After I do, how to I get to Makuhita's Dungeons?
A: I believe you’re talking about the training areas. Go to the southern end of the town and there should be like a temple thing, attempt to walk in and you will be forced to choose an area.
Q: Grr! I can't find out where blue team is, any advice?
A: I’m slightly confused about that. Can you please state which part of the game you’re in?
Hope that helped!