Prism can plot error bars directly from raw data. Prism lets you enter SD or SEM if you have calculated them elsewhere, but there is no need to do so. Enter your raw data, and let Prism do the rest. Prism offers analyses that perform row and column descriptive statistics, but these are only to help you understand the data. You do not need to run these analyses to plot error bars.
If you made a mistake, or want to try different analysis choices, you can always return to the analysis parameter dialogs. Don't repeat the analysis unless you want two copies of the results. To open the analysis parameters dialog, click the analysis parameters in the upper left corner of any results sheet or in the toolbar.
Select any block of tabular results, copy to the clipboard, and paste onto any graph or layout. This will be a live link. If you change the data, or the analysis choices, the embedded results table will update.
Many analyses (i. e. Transform) create results tables that can be used as a data table. These results tables have green grids, unlike tables with red grids that contain tabulations of results that cannot be graphed. From any results table with a green grid, click Analyze to analyze the results. You can make the analysis chain as long as you want. For example, you could Transform, then Normalize, then fit with Nonlinear regression, then transform the residuals from the regression.
By default Prism copies graphs to the clipboard in both (Windows Metafile) and EMF (Enhanced metafile) format. and lets the pasting program decide which one to use. You can tell Prism to only copy one format (File & Printer tab of the preferences dialog). If graphs pasted into other programs don't look right, try all these settings.
You aren't stuck with the sheet names that Prism assigns, or their order. Rename or reorder your data tables (and graphs...). When you rename data tables, linked analyses and graphs are automatically renamed. Delete sheets you no longer need.
Some people make the mistake of starting a new project for every data table, not realizing that a Prism project (file) can have up to 500 data tables, analyses and graphs. You can keep an entire project in one file.
Don't define 'project' too broadly, because a huge project can be hard to navigate. You can always merge projects later, or include a graph from one project in a layout of another.
If you want to change your mind about analysis choices, you can do so. You can change the parameters (options) for the analysis. Or you can change which data table and which data sets are analyzed. There is no need to start the analysis again, which leaves an obsolete copy of the results in your project.
Prism automatically makes a graph of each data table. So when you want to make a second graph of that same data, people commonly copy the data and paste onto a new table which is automatically graphed. No need for that. You can make any number of graphs from the same table. Just click the New button, and then choose Graph of Existing Data.
We call a Prism file a "project", but you can decide how large to make it. Huge files can be hard to navigate. So it often makes sense to keep files of reasonable size. You can always merge projects later, or include a graph from one project in a layout of another.
When working on a large project, do more than backup the current version. What happens if you mistakenly delete key data? What happens if the file someone gets corrupted? Use Prism's Backup command to save interim versions as you work.