There are two great mods that alter whiterun and i am trying to make them compatible with each other. I am completely new to modding. When i load the editor i am selecting both of the whiterun mods. I am basically just needing to delete or slightly move tree's and foliage so, pretty simple. First question i have is when i go to select some tree's they are not showing up in the cell view list so that i can delete them, i figured this has to do with which mod is set active but wasnt sure how that works. actually i dont understand how the "set active" works at all, second, is there a way to create a new esm file that contains the altered tree and foliage data that i can load after the two mods while i am playing? or is it better to just resave one of the existing mods? The issue i am worried about is if one of the creators updates their mod i dont wanna have to go back in and hand move stuff around again so i figured having my changes in its own esm is best but i dont know how to go about saving my own esm. Thanks in advance for any help/suggestions!

First person to help could win cash and prizes!

...darn subjunctive trickery everywhere...

uhm....
what exactly does "when i go to select some trees" mean? do you already _see_ these trees in your render window and have selected them, or, well, whatever else?
if you do NOT see them, select whiterun world in cell view window and double click one of the cells in the list to load it into the render window.
if you DO see your trees there and have already selected it, but just don't see it in cell view list, your camera view point obviously is in another cell than the tree, if this is the case, keep your tree selected and press 't' for "top view", brings camera right above selected object = definitely in same cell, you'll see your tree selected in cell view list now.
you can also press 'b' to toggle cell borders, makes orientation easier in exteriors.

for deleting the trees, better don't, but set them to "initially disabled" in their reference data tab (they'll still be visible in the editor though, but you can just move them out of the way to whereever, won't be visible in game as long as they're disabled).

for you set-active-thing: no idea what you mean.

and for your esm-thing, to make your mod change (== dependent of) the two others, those would have to be esm's themselves (if this should be no longer true in skyrim, somebody correct me please), which they probably aren't if you have them from steam, because steam seems to mercilessly esp-ify everything it gets in its claws , so that's a tough one

you ever thought about hitting up the mod authors about making them compatible themselves? or offer them to send over what you already changed anyhow or whatever?

I think I got everything figured out, one thing im still confused about that i think maybe you touched upon.. If a person creates a mod that adds 10 new rocks, can i not make a new mod loaded after theirs that moves their rocks? Or can you only move things around that are in esm's and not esp's? Thanks in advance for the clarification.

sorry, but actually _clarifying_ this is currently beyond me.
what i can tell you is: up to fonv, it was: you want to modify mod a via mod b -> mod a has to be esm. full stop.
(or, you'd have to undertake some quite adventurous scripting journeys to still make it work on an esp-basis - if you were stubborn enough to not accept a no-go just so, like me
for papyrus, i'm far from being able to tell what can or can't be done, but i've read at least so much, that there's at least one way for esp-communication, that uses form lists.
anything from here on is just blind guessing until someone happens to come along who can actually explain this.
maybe you just have to put your trees4change in a form list and have everything in there checked if still disabled onupdate, or whatever, really don't know.

okie dokie, thanks for the help!

You want to create a new esp with the two mods as masters. (Though I think they need to be esm).
Making making a mod "active means you are working on that mod and the CK will load all of the masters required by that mod.
When other esms are checked, the assets / resources of those mods are available to use / edit in the active mod.

So Skyrim.esm, Update.esm, WhiterunMod2, and WhiterunMod2 should be checked.
Do not make active any other mod. Load the CK. When it's finished loading, Select File>Save>"YourNew.esp".
Any changes you make should now "patch" the two Whiterun mods to reflect the changes you make.

The next time you start the CK to edit "YourNew.esp", make it active and the CK will load all of its masters along with it.