I designed this character with his arms along his sides. I gave him bones and put a lot of detail work into getting everything right. I now want to add clothes and am running into issues because his arms are along his side and not spread out so the shirt wants to go through itself. I was wondering if there is a easy way to make his arms rotate up and the bones follow with. I want everything to stay in exactly the same position relative to each other because some of the bones are in fingers and a little shift will be bad.
This is actually two questions (probably more): The first is using weights to connect the bones to the mesh. This is done in Weight Paint mode. Here's a link to several answers which would help: https://blender.stackexchange.com/search?q=Use+Weight+paint+mode
The second is moving bones; which really just consists of selecting a bone, and moving it in a pose. However, this is related to parenting the bones and weight paint: https://blender.stackexchange.com/search?q=Parenting+bones
Possibly a third question regarding adding clothes; but, you should try to ask only one question at a time. I realize with moving bones, this doesn't appear to be a multi-question problem. Hopefully these links will help.
I've never had to reset the pose like you mention, but, I searched for information on how to change the pose and make this and the deformed mesh the default. It says here that this presumes the weights are properly set and the deformations on the mesh work properly. Credit goes to NixArt for this information.
"This procedure supposes that you have already rigged and weight-painted your object so that it deforms correctly. At this point, you simply want a different rest pose for your object. However, when selecting “Apply Pose as Rest Pose”, you do not want to waste your time correcting your mesh and redo the weight painting for your new rest pose. Here is how you can do it:
Select your armature and go in “Pose Mode”. Pose your object in your new rest pose. Go in “Object Mode” and select your deformed object. In the object’s “Object Modifiers” stack, copy the “Armature Modifier” by pressing the “Copy” button. You should have two “Armature Modifiers”, one above the other in the stack, with the same parameters. This will deform your object twice, but it is ok. If you go in “Edit Mode”, you will see that the mesh has been deformed in your new rest pose. Apply the first “Armature Modifier” (the top one), but keep the bottom one. The latter will replace the old “Armature Modifier” and will allow to pose your object with respect to your new rest pose. At this point, the object will still be deformed twice. That is because we need to apply the current pose as the new rest pose. Select your armature and go in “Pose Mode”. “Apply Pose as Rest Pose” in the “Pose” menu. This will clear the double deformation and put your object in your new rest pose." - NixArt
and possibly this tutorial