Hi Vikas,
Sorry I did not reply earlier. Your original email prompted me to develop a more functional workflow.

I have developed a few functions that make organizing research much easier. I have functions that reorganize, rename, and add links to pdfs, search for and add links to pdfs that have been organized by other programs (Papers2), import notes from Skim, rename org-bibtex headlines to a format I find more useful (e.g. Author (year) Title), and do a few other things that I find convenient. The renaming functions also look up crossrefs, and the headline renaming function lets you know if they are missing. The functions are partially documented and have a few customizable functions so they can be set up for different systems. Also note that the pdf organizing system uses the conventions of my old research organizing tool (Papers2) but this can be modified without too much work. I have attached a file with the functions. The bottom of the file also contains the variables that I have set and hooks that I have added to make the functions integrate more smoothly into my set up. They may serve as a guide if you choose to use them. 


Additionally, here is the capture template I use for bibtex entries, it is based largely on Richard's but it has you import more bibtex info during the main capture process, and uses a function to help you find crossrefs.

("r" "Reading" entry
         (file+olp "~/Google-Drive/Personal-Projects/Bib/Readinglist.org" "RLIST Inbox")
         "** %^{Todo state|READ|FIND|PRINT|NOTES} [#%^{Priority|A|B|C}] New Reading Entry %? %^{BIB_TITLE}p %^{BIB_AUTHOR}p %^{BIB_EDITOR}p %^{BIB_YEAR}p %^{CUSTOM_ID}p %^g
:PROPERTIES:
:BIB_BTYPE: %^{Entry type|book|article|inbook|bookinbook|incollection|suppbook|phdthesis|proceedings|inproceedings|booklet}
:ENTERED_ON: %U %(my-org-bibtex-crossref)
:END:" :prepend t)


When I have some time I will follow up to explain how the functions work in more detail. In the mean time let me know if you have any questions. 

All best,
Leonard