How to clearly lay out research ideas A constant struggle for most graduate students is how to clearly lay out research ideas in a coherent manner. We are constantly in the "weeds" reading papers, move data around, running models, and researching tiny little details. When we decide to come up for air and begin to talk about our ideas they are unorganized and unclear. We assume people know what we are talking about and so we talk right past them. 

So my question is, how do you clearly and coherently lay out research ideas? 

Are there books to help with this, or other resources? Are there ways to overcome this challenge as a researcher?
Big ideas


Think about breaking your big ideas down into manuscript ideas--what would be the focus of each paper you could potentially write? This helps to break big-picture research topics down into both manageable and focused sub-topics, and will help you plan the even smaller research steps needed to achieve the bigger goals. 


So for example, if my big grand research question is "Why are all my houseplants dying and how do I save them?" I could foresee breaking that into manuscripts:


Review of common houseplants with compiled statistics on hardiness, common stresses, etc. and development of new quantitative metric for normalized houseplant stress level
Experimental results of houseplant responses to induced stresses
Application of a new methodology for protecting houseplants from common stresses.


Similarly, break your smaller sub-projects down by what results you'd like to attain (e.g., figure comparing x and y as a function of z, calibrated equation describing x(z), etc.), then plan your work around reaching these goals.
Keep your notebooks organized according to these big ideas (e.g., Plants Notebook).
The front page of each of my notebooks is a running to-do list of things that are relevant right now, which I try to review and update at least once a week.


Smaller ideas


Make sure your smaller ideas fit in under your larger research goals/plans above, and record your ideas in the appropriate subject notebooks
Keep a "parking lot" notebook for your random thoughts and ideas that might not be tractable/relevant right now but might someday be useful.


General


I like to use a digital notebook app instead of a paper notebook to keep things organized since you can move text around as needed... my old paper notebooks are full of notes on different topics all mixed randomly so it's hard to find them again, and relevant notes are often in very different places. You can keep different notebooks for different topics, but I've found it's still hard to keep things organized and the topics themselves often evolve over time.
Go back occasionally and re-read/reorganize/rewrite your old notes. This is especially facilitated by using digital notebooks because it allows your notes to be more of an actively updated list of relevant things you're working on right now (for the most part), rather than a bunch of disjointed things you randomly wrote down way back.
In addition to (digital) notebooks for each subject I'm researching, I also keep notebooks for seminars/conferences/meetings/workshops (since they're often on random topics unrelated to my research), administrative/proposals, outreach, teaching, classes, and papers (notes on papers I've read). Any info in one of these that's also relevant to a research project, I'll copy over to that subject notebook (this is a little clunky and would be easier if I could find a notes app that lets you cross-reference or alias pages to multiple notebooks...).