Omniscope will automatically update blocks when it detects the files have changed. So if your sources include an Excel spreadsheet which has been updated/saved since you first imported, a refresh will be triggered, which will percolate downstream through all your operations, and require other sources to be opened in order to use their data in combination with the updated data.

You can customise Omniscope to observe changes less frequently using the menu for the block in question, choosing "Update options".

You can also insert "breaks" in a model, by identifying a large independent section of sources and operations with a single result block, adding a File Output block, clicking Publish, and replacing the link downstream with a link from a new File source block for that file. This "break" uses a file to store the results of the upstream operations and sources, allowing you to control when they are "re-Published" and propagated further through your model.

You may also consider increasing the DataManager disk cache. For this and other suggestions see:
http://forums.visokio.com/discussion/1258/datamanager-loading-time-/p1
http://forums.visokio.com/discussion/comment/4514/#Comment_4514