Once across the river, there are two options available. One along the NE bank of the river, the other through the city. The latter might require a bit more attention, but has the advantage of taking the pilgrim past three of the churches in the Baixa/São Bartolomeu area, the lower part of the city. Note, though, that if you want to visit the Se Nova and Se Velha, these will need a side visit to the area near the university, the Alta. That is a steep climb no matter which way you go.
Some Fatima pilgrims use the SW bank of the river, crossing at one of the road bridges at the northern end of the city before heading southwards. They will be going the other way to you if you do see them. I don't recall that being waymarked on the way into town on the CP route. There is also at least one other route through the town that is marked up for Fatima pilgrims, but I have not checked where it goes. It might take them past the cathedrals - it seems to come down from the Alta, the high section of the city near the university.
Once the CP leaves Coimbra going north, there is only one path that I am aware of between the towns. While there will only be one path in most towns and cities, you will inevitably deviate in places to get to your accommodation or to find somewhere someone has recommended for a meal.
I have walked both the Central route (from Porto) and the Variante Espiritual (from Valenca). They are both interesting routes, but I haven't walked any of the other three routes heading north from Porto. I am not really in a position to offer a comparison for you.