Background: The basic idea is to use a word processor (eg MS WORD) for the text and any image program (eg Photoshop or Illustrator or any other) for the figures. You save all of your text files and figure files in single folder. The InDesign document is created so that it contains links to these files. You do not want to embed the text and figures but to link them, so that when you revise the word processor file or edit the figures file, the edits will then appear in the InDesign document. When you update the files, you just tell InDesign to update the links, and it produces a document with the new version. The advantage of InDesign is that it produces perfect pdfs, that it allows you to resize figures etc with no loss of resolution, and that (unlike MS Word) it allows you to place figures and legends where you want them to stay. However, InDesign is really complicated and poorly documented, so it is necessary to remember some Tips and Tricks.
First make the inital versions of your text and figure files.
Then create the new InDesign document, with the correct paper size (66p x 51p = 11" x 8.5") and margins (3p all around = 1/2").
Make sure of one important setting: In Edit > Preferences > File Handling (Windows) select "Create Links When Placing Text And Spreadsheet Files". If this option is turned on, then you can use the Links panel to update, relink, or remove links. If this option is turned off, text files are embedded (not linked).
Place the text file into the into the document using Place-Shift-Click. (Shift-Clicking makes the text automatically flow onto successive pages, adding new pages as necessary). Choose the "T" text tool, and the do Edit > Select All and then choose the font and size and vertical spacing, which for grants in Arial Regular 11 size and 12 vertical line spacing. The document will then have the NIH standard of 6 lines/inch, .5 inch margins all around, and 15 characters/inch.
It is easiest to create frames for the figures, and to show the text wrap window and click the selection that makes the text wrap around the boundary of the frame. The empty frame tool is a rectangle with diagonal lines across it. Then you can place a graphics file of almost any kind with the File > Place (Ctrl-D) command.If you click into any empty frame, the graphics object will fill the frame. Alternatively, you do not need to create the frame first, since placing a graphics object on the text by clicking its upper left corner and dragging down and right will automatically create a frame around the inserted graphic, which you can see when you make the text wrap around the boundary of that frame. These placed graphics will all be linked rather than embedded into the document.
Note the difference between the different tools, one for changing the content and the other for changing the frames. The Selection tool allows you to select text and graphics frames, and work with an object using its bounding box. The Direct Selection tool allows you to select the contents of a frame, such as a placed graphic, or work directly with editable objects, such as paths, rectangles, or type that has been converted to a text outline. See Overview of selection methods in InDesign help for more information.
To add a legend to the bottom of a figure, create an empty frame the top border of which is exactly on the bottom of the Figure's frame, and then place the text file that contains the legend, and finally change the font size, etc, to be the size you want for the legend. If you then select both the figure's frame and the legend's frame and click Object > Group, the two frames will be joined, and you can drag them around together as a single unit.
Note that the document prints perfectly even though the figures that are displayed while you are placing them are quite low resolution. You can also save the printed version as a pdf instead, the normal thing for grant applications.
--Michael Stryker July 2, 2010