A few pointers I picked up along our application process (well I wasted $$$ before)...
1. She has a visa already - I surmise she has a client ID.
2. If both of you are in Canada, use CIC's online application process for in-country applications - processing is much faster than a paper application. You will need the Client ID to login.
3. You can always send a paper application, but if you look at the processing times, paper applications take much longer.
As this is a work permit application, I would advise that you download the latest paper forms from CIC - especially the guide as reference. They usually update every few months.
She is now the one declaring the common-law union (you did not during your work permit application) - she will have to using form IMM5409E (paper application). There maybe some additional requirements needed to show proof of CLU - to take note of it. If using the online application - take note of the section 'Marital Status' - there may be a drop-down menu to select CLU.
Another thing - the marked difference between the paper application and the online application is that the doc checklists are different. The online application provides you a shorter list of documents you have to attach/upload. The paper application gives you a checklist - but allows you to add additional documents in support of your application. You can also do this on the online application, but it is not stated - so a lot may err in just uploading the listed documents and not adding in supporting documents which can aid a lot in getting the work permit approved.
It does not hurt for you to create a letter in support of her application - you as her spouse requesting approval of a work permit for her. You may describe your relationship, your current work status, your company and your position, and your plans to apply for PR and settle in Canada. You can also state there also the reasons why she was not declared initially in your work permit application as CL spouse. Anything which can help but do not overwrite - 1-2 pages should be enough. Make it compelling as if a story.
Same for her - but for her it will be a preface letter to her application. Essentially stating the reasons why she is applying and adding details about your work (i.e. you have a contract/employment with a company, you and her have been in the country for x years, entered the country under what type of visa. These details which will be reinforced by later by your own letter included in the application.
Now sending it - it depends on your choice, paper or online application. For paper applications, any supporting document that you think will show proof of your work, her work, both of your status, your union, add it. Make sure you also mention these documents as part of your application - work it in your letter. This is to draw the attention of those in CIC to read through these supporting documents base the approval using all of the available information you provided.
If you use the online application - the system prompts you only for documents you will need to upload. I suggest you scan any supporting documents (your letters, her letter, etc.) as part of a single file and uploaded as the first document in the checklist. This is to ensure that when CIC reviews it, the first file they download includes already these supporting documents, and it will be included in the first pages they review when looking over her application.
Also, for explanations on CIC's online application, there is a limit on the number of words. Make sure you have MS Word or Notepad to just copy and paste and further edit your explanation. This saves you the frustration when CIC refreshes in the middle of your edits or if your explanation exceeds the word limit.
Paper application - use registered mail/courier. Makes sure you can track the receipt of your application and gives you peace of mind somebody received it.
\Good luck and bless you both in your application!