One of the biggest headaches early on in learning HOI2 is learning to reorganize the units into what you want. To someone not used to the operation, this can be a headache. I'm posting this short explanation of how to do it for all to read.
As far as land units and naval flotillas go, you can reorganize between two groups in one movement by drag selecting the units, then using SHIFT+CLICK to remove the units you don't want to reorganize between, then click the box with a double headed arrow in it. This will only work if you have 2 corps/flotillas selected.
As far as the air units go, if you've patched, there is a maximum of 4 units per stack. If you want to select air units with ground units in the same province, select an air unit from the province forces list (or left click through the stack until you have an air unit selected), then SHIFT+DRAG a box around the air unit to select the entire stack. Then just SHIFT+CLICK to remove extraneous stacks. Now, if you have more than 4 total aircraft in the two remaining groups, you can't merge or reorganize. I.E. A group of 3 and a group of 2 won't let you reorganize between the two, even though neither is full. You would have to break 1 aircraft wing off of one of the groups (3 and 1 or 2 and 2) before you could do any reorganizing.
Easiest solution I would suggest is to deploy directly to formations. Figure out an army/air force/navy organization, and set them up. Then, as units come off of the line, deploy them directly into a unit instead of into a province. This should keep later reorganization messes to a minimum, and any reorganization you do can be much more efficient because you know what is where, and can select just those groups much more effectively.
As far as land units and naval flotillas go, you can reorganize between two groups in one movement by drag selecting the units, then using SHIFT+CLICK to remove the units you don't want to reorganize between, then click the box with a double headed arrow in it. This will only work if you have 2 corps/flotillas selected.
As far as the air units go, if you've patched, there is a maximum of 4 units per stack. If you want to select air units with ground units in the same province, select an air unit from the province forces list (or left click through the stack until you have an air unit selected), then SHIFT+DRAG a box around the air unit to select the entire stack. Then just SHIFT+CLICK to remove extraneous stacks. Now, if you have more than 4 total aircraft in the two remaining groups, you can't merge or reorganize. I.E. A group of 3 and a group of 2 won't let you reorganize between the two, even though neither is full. You would have to break 1 aircraft wing off of one of the groups (3 and 1 or 2 and 2) before you could do any reorganizing.
Easiest solution I would suggest is to deploy directly to formations. Figure out an army/air force/navy organization, and set them up. Then, as units come off of the line, deploy them directly into a unit instead of into a province. This should keep later reorganization messes to a minimum, and any reorganization you do can be much more efficient because you know what is where, and can select just those groups much more effectively.