Well, the goal is to rename setfiles (the zips) and sometimes the romfiles too (files inside), depending on each set. That said renamers are free to use any tool as long as it produces correct dats.
Long ago there was a part of tim called "renamers tool" where you could insert information on a form for each of the desired flag and it would generate the complete setname for you (and rename the zip too i think). Although this may sound useful, especially for newcomers, the renamers never used it since it introduced a lot more steps to rename something so they just rename sets directly (renaming the zip/files or even editing the datfile itself.
To generate datfiles most use one of the tools you named (most use clmpro, TIM is outdated). The process consists in indicating the folder where the sets are, adding the header details to the program (datfile name, authors, version, category and such), a few more details and pressing "create".
This was just a brief introduction, current renamers use anything they feel comfortable, some their own tools, others renaming the setfiles or directly on datfiles. You may want to check their opinion or tips since i don't rename much (or anything) myself.
An example:
Start with a datfile (eg. MSX MSX2+ - Various (TOSEC-v2009-09-01)) and all its sets.
Checking the existent sets for mistakes, to fix one i could:
1) Edit the respective zipfile (and the file inside it if needed), then i would need to generate the datfile again.
2) Open the original datfile on any *decent* text editor and edit the correct entry (make sure you don't break or rename anything wrong here), update headers.
To add a new set it is simply a process of renaming it and adding it to the correct folder + generating the datfile (or alternatively creating the entry manually, in this case this isn't a great option since you need to get the crcs/md5 and so on).
That's it, got it? The process is simple, just playing with the sets, renaming the files and generating the dats, moving them or separating them in different categories (folders) and creating the respective new dats to replace the older ones and so on (for example, MSX MSX2+ - Various probably could/should be split into various folders: Games, Demos, ...).
So, what do you think about the process? My main suggestion to anyone starting is to take a look at TOSEC Naming Convention first, try to create a small test datfile with 2 or 3 sets and later doing an update to it just to get how it works. It shouldn't be anything hard at all.