You can create unique guidelines on each unique page. Just drag from the rulers (if you don’t see rulers on your “page stage” select View > Rulers, Grid and Guides… > Show Rulers) and those guidelines will only show on that page. If you want a global guide, hold the Ctrl/Cmd key while dragging from a ruler. Or, you can create guides numerically via View > Rulers, Grid and Guides… > Create Guides… and uncheck the box, Create as Global Guides.
You can’t create or choose from multiple sets of global guides. Guides don’t “come across” in masters or library widgets/templates. What I’ve done for projects like yours is to create a few template pages, complete with guidelines, colored columns, measurements, etc. and place those at the bottom of my pages list, under a folder named “Templates” or “Other”. When I need to add a brand new page to my prototype, I duplicate one of those template pages, name it and move it up in the list. When publishing your prototype you can choose not to include those pages (but it shouldn’t matter, really.)
If you use the approach of using masters and creating line widgets for your makeshift guides, I recommend putting them all in a dynamic panel (or group them all). For that dp or group, assign a Loaded interaction of “Hide This Widget” so that it will automatically hide itself in the browser. You can also use the “Hide from view” checkbox in the Outline pane to toggle visibility in the editor.