You will need Entity Beta 1.1.5 or higher, which can be found on This Page.
Part One: Cloning Chunks Within A Reflexive
Cloning chunks within a reflexive, will add the desired number of chunks, of a certian type, to the selected reflexive. It will exactly replicate the selected chunk, and add as many as you want to the end of the reflexive. (This is widely used to spawn more machines, scenery, and obstacle spawns in the Scenario tag in many of the latest mods).
Cloning chunks is very simple with Entity. Navigate to the tag you wish to add chunks to (I will be using the [scnr] tag), then navigate the main reflexive that you wish to add chunks to (I will be using the Netgame Equipment "ITMC" reflexive). In the Refrence Editor, right click on the reflexive, and select "Clone Chunk"

Now, a new form, Chunk Cloner, should appear. Get to know this form, as you will find it one of your best friends when making mods...

Back to the tutorial, lets say I want 10 more Warthogs to spawn on Coagulation.
First, I would find a warthog spawn (which just so happen to be located in the Netgame Equipment reflexive), and select it.

Then, to the right of the treeview you should see a textbox labeled "Ammount of Chunks". Make the ammount the number of chunks you want to duplicate, in this case, 10 chunks for 10 more hogs.

Once you have entered the desired ammount, hit the "Clone" button, and wait for Entity to do it's thing. You will now see 10 more warthog chunks than before in the treeview.

When you are done adding the desired chunks/reflexives you want for each tag, hit the "Add Meta to Map" button.

Part Two: Adding New Reflexives to Tags
Now, lets say we want to put a Covenant Watchtower on Coagulation. The only way to make machines spawn "Activated" is to spawn them through the Machine Placement/Machine Pallete reflexives of the [scnr] tag. Last time I checked, Coagulation did not have any machine reflexives, so we are going to add some. I am going to take the Machine Palette and Machine Placement reflexives out of Relic, and put them into Coagulation (since the Idents are already set to the Watchtower).
Note: When adding reflexives or chunks from other maps, make sure you transfer the refrenced tags (in this case the Covenant Watchtower [mach] tags) to your map before you add the new chunk or reflexive.
First, in Relic, I am going to delete the un-needed chunks (The ones not used to spawn the Watchtower) to make the map a bit smaller. If you wish to do so, simply select a chunk, and hit the "Delete Reflex/Chunk" button.

So, for each reflexive I want to add to Coagulation, I need to select the reflexive, then hit the "Copy To Clipboard" Button. (In Relic)

After you click "Copy to Clipboard", go into the Chunk Cloner of the map without the reflexives (In this case Coagulation), and click on the first reflexive you see at the top.

Once you have selected that reflexive, hit the "Add to Selected Reflex/Chunk button.

Now, you can see the new reflexive in the meta tree of Coagulation.

Do that for both the Machine Palette and Machine Placement reflexives, move your spawns, and you can now have fully functioning machines on a map without the Machines reflexives.

Part Three: Adding New Chunks To Reflexives
Adding chunks to reflexives, is about the same as cloning chunks. The only diffrence is that you can add chunks from one map to another, and add chunks from diffrent tag types. Anyways, what we are going to do, is add a new machine chunk to Ascension (Which already has machine reflexives), to spawn a Zanzibar gate.
So first, open both maps in Entity, and goto the Chunk Cloner in Zanzibar. Find the Machine Palette reflexive (within the [scnr] tag, then the House Gate chunk. With that chunk selected, hit the "Copy To Clipboard" button.

Note: If you have not added the tag in the new chunk your adding, you need to add it to your map (In this case Ascension) before you continue to the next part.
Now goto the Chunk Cloner in the map you want the new item in (In this case Ascension) find the Machine Palette reflexive (within the [scnr] tag). Click on that reflexive, then hit the "Add To Selected Reflex/Chunk" button.

Wait for Entity to do its stuff, then repeat that for the Machine Placement. If there is a palette and placement reflexive, you will probably need to re-link them together in teh meta editor, depending on what you added, and where.
Part Four: Overwriting A Chunk or Reflexive
Overwriting a chunk/reflex, will replace an existing chunk (or reflexive) that you have copied to the clipboard. This can be used for a variety of things, like you could use it to easily replace the teleporter and gate on Relic, with a Covenant Watchtower. Another thing I have found it useful for, is to "save" your spawn locations, if you wanted to re-do a mod. Take this Bridge BSP Conversion...He "took" the spawning locations from 03_Oldmobassa.map, and added them to Gemini.map (With the bridge's BSP) This is also the only method I have seen to spawn [scen] in the Scenery Palette reflexive, and have it keep it's collision.
Lets say I made a new map out of machines, such as Citadel. After I had everything where I wanted, but I made the map over 80mb, so my xbox wouldn't load it anymore. I could take the chunk data from that map, and apply it to a clean map, and all the spawns would be the same.
So to overwrite a chunk, open your two maps then goto the Chunk Cloner on the map that has the chunks you want. (In my case, I have open 2 Ascensions, One with a bunch of machines spawned, and a clean one). Select the reflexive (so you don't need to do each chunk one-by-one) that you wish to have on your new map. Then hit the "Copy To Clipboard" button.

Note: Make sure that any tags that are refrenced in your chunks are in your new map, or you will get errors when doing the next step.
Now, go into your other map (In my case the clean Ascension.map) and open the Chunk Cloner. Select the same reflexive you did in the other map (In my case the Machine Placement), then hit the "Overwrite Selected Chunk/Reflexive" button.

Now, Entity will make all spawns in that reflexive, the same as they were in my other map.
Part Five: Deleting Chunks And Reflexives
Entity has a nice little feature that will let you remove unnesessary chunks. This can be useful in keeping your map size down, so that the resulting patch will be smaller.
To remove a chunk or reflexive, simple select it in the Chunk Cloner, and hit the "Delete Chunk/Reflex" button.

Note: Every time I have tried removing chunks, Entity later give me the "Broken Ident" error. I'm not quite sure what that error means..but it probably isn't good. >_< (However even though I get that error, my maps always seem to play fine.)