You need the spacing between the UV islands to make sure that none of the shadow information that is baked into that texture is bleeding onto any other UV island. The higher the lightmap resolution that is set will help get better shadow information as well.
The two UVs are completely separate in this respect. The diffuse can be setup however you need your texture to be represented in the game. This means you can use overlapping UVs with no consequence if this is what you need for your asset. With regards to lightmaps you do not need to worry about the rotation of the object based on the diffuse texture. This UV is solely used to bake shadow information and shadows/lights that are cast onto your asset. Because this is using the scene lighting and shadow information will not directly affect your UVs layout. (ie. having a polygon rotated upside down will not cause your shadow information to be upside down on your object when it is baked)
Take a look a the World of Level Design tutorials I linked above. This will handle a lot of the concerns with Lightmaps. This will give you the basics and the best way to get a good look with lightmaps. They provide some images for different setups of lightmaps to demonstrate why certain layouts work better than others.
Tip: Make sure when laying out edges that they are setup to be on a grid point (this is in one of those tutorials) because anything that falls in-between a grid space will get more shadow information.
This certainly is one way of doing it. I just use one UVWunwrap modifier though. I just switch between the two maps by choosing the channel I want to modify then choose Abandon when switching between the two. This sounds like it’s bad but it’s really just moving between the two and leaving the changes you made to the UV Layout.
Depending on my model, I typically get a general layout in my channel 1 then save the UV layout to a file so I don’t lose it. I’ll switch to channel 2 then load in that UV layout file and edit it down to what I really need to be specifically setup for my lightmap.
If you have any other questions along the way let me know!