As one who frequently reviews submittal packages I will tell you this.
If you're submitting a printed package, follow the binding requirements in the specifications.
Group similar equipment into tabs or sections. I.E. AHU's together, terminal boxes in a separate tab, pumps, tanks, fans, etc. For items such as ductwork, insulation, piping; one submittal for the all ductwork, insulation, piping is usually sufficient provided you include each type of duct, insulation or pipe.
Do clearly identify what piece of equipment your submittal is for. If this is not done, I will not hesitate to return the submittal marked "REJECTED".
If the submittal sheet you are providing includes multiple models of a particular item, highlight the model or include notes to clarify what exactly you are submitting. This may also result in a Rejected submittal if not done.
There is no rule or standard to an order in which to organize the tabs/sections. However, I have grown accustomed to having large equipment (AHUs, chillers, condensers, etc) first followed by terminal boxes, fans, pumps and other ancillary equipment. Bringing up the end of the submittal is typically minor equipment such as ductwork, insulation, valves, dampers, etc.
Including a table of contents is invalueable as a cross check that everything is included.
As for software, Adobe Acrobat Pro has all the tools you need. There is probably other software available, but I do not know what it is.
(The more you do identify what you are submitting and make the package easier to navigate using tabs and bookmarks, the more likely I am to give you the benefit of the doubt if you accidently miss something. I'm more like to give you an "Approved as Noted")