This might be a stupid question, but if you *knew* in advance that the photos would have to be square to fit the album template, why didn't you bear that in mind when you took them? OK, I know that doesn't help you right now, but next time...
I'm finding it hard to know what to suggest about your current problem though, without seeing what the finished pages are supposed to look like. If the template puts any kind of border around the images, then padding out a rectangular image to fit within a square border will look incredibly stupid. But if not, then padding out a rectangular image with white edges either side, and placing it on a white page, it won't necessarily be apparent what shape the image "should" be.
One thing I'd suggest, though, is mixing things up a bit. If you crop 90% of your images to be square and leave 10% rectangular, that probably won't look good - it will be obvious that they are all supposed to be square. But if you create a good mix of squares and rectangles, or leave them all as rectangles, it won't be obvious what you've done.
Finally, I'm sure I'm not the only one here who's thinking that if you could post a couple of examples (screen shots perhaps) of the templates you're using, it will make it easier for us to suggest ways to approach it.