While the two are related, it is probably easiest to start with thinking of the complaint and the MSJ as separate and unrelated.
The MSJ is a motion that attempts to either (a) get a judgment in the Plaintiff's favor on a cause of action, or (b) defeat a Plaintiff's cause of action based on an affirmative defense. Most MSJs are directed to all of the causes of action in a complaint, or affirmative defenses in an answer, but occasionally they are made on only one cause of action. (MSJs are different from "motions for summary adjudication" which only seek adjudication as to a legal issue, or multiple legal issues, not the entire cause of action, however I note this as they are often filed together).
Defendants most commonly bring MSJs as they attempt to defeat a cause of action based on an affirmative defense (say statute of limitations), and can do so by showing there is "no triable issue of fact" as to when the incident occurred, when the plaintiff first discovered the injury, and when the complaint was filed. There may be legal arguments about how this should be interpreted, but if these three facts are either agreed upon, or so clear that there is no reasonable dispute, a court can rule on the motion and the plaintiff may lose that cause of action, or the entire case.
For a party opposing the MSJ, the standard is merely to show that there is some fact that the moving party is relying on that is subject to reasonable dispute and therefore the matter is subject to a jury trial (or a bench trial).
The motion that you are opposing should be dealt with within the factors and scope of the moving papers. If there are causes of action not identified in the motion, you may need to deal with them at trial if the matter goes to trial, but you do not need to deal with them here. If you have affirmative defenses that are at risk, you need to address those as well. It is key to look to the facts (READ: ADMISSIBLE EVIDENCE) and see what is in dispute, what they failed to introduce, if there is any objection to their evidence (some statements that are put into evidence really aren't evidence at all, just hearsay or statements by counsel).
The Complaint has allegations of fact, if you file a lawsuit and allege fraud, breach of contract, but not negligence, a defendant can defeat your case tactically through defeating the fraud and breach of contract causes of action, even if you have a good cause of action for negligence - you just forgot to include it. (Obviously there are ways to address this, but I am just using this for demonstration purposes). In your complaint, you need to allege facts that support each of your causes of action, otherwise the complaint can be subject to demurrer, motions to strike, and motions for summary judgment. However, as you litigate the case, discovery and investigation often brings in new facts, or uncovers new issues. You do not need to amend your complaint each time that these new facts come to issue, unless you are trying to add a new cause of action or new affirmative defense. The only time that you are required to change your pleading to conform to new facts would be after the other party has made a motion to strike your complaint or a demurrer, or some other motion which requires you to amend your complaint (or parts of it) due to a lack of specificity, or some other defect, which you can address with the additional fact pleadings.
I have not read your papers, but I believe you are under a significant motion for summary judgment here. To break down the tasks before you draft the opposition to the motion, first review the facts (or separate statement of undisputed facts) upon which the motion is based, see what you agree happened, see what you disagree with; second, look at the evidence that is being introduced, is it properly "authenticated" this motion requires all of the facts or exhibits that they are attempting to introduce to be authenticated (usually through declaration of someone with firsthand knowledge of the document at issue, for example), this is true with all motions, but this one in particular given its nature; third if there are objectionable exhibits that are being used as "evidence" note them down and come back to them to see what the proper evidentiary objection would be; fourth review the papers and see what the major arguments are and points you need to address (usually there is a common theory of law that you will need to address), and fifth, begin drafting your opposition.
This flow sheet is something I have used, it may be helpful to break down the tasks when addressing your own (opposing an MSJ can be overwhelming even for counsel).