Can I just fly or soar to my secret base, since it's in the middle of a route and takes effort to get there. Or do I just have to bike and HM to it every time I want to go to my base
There is only one secret base you can fly to: Secret Islet. That's where my base is, its to the left of sotopolis after a dive. Other than that, sadly no.
You can only Fly to the route/area that your base is in, not the actual base.
So yes, you have to use HMs and bikes.
But it would be good if you could go straight to your base.
I just tested it with Fly; you can select the individual base by going to the AreaNav and selecting"Bases", then select "Fly", but it will only take you to the route and not the individual base. Soaring is the same because I've tried it before. I'm afraid you're going to have to take your HM slave to get to your base. I know how you feel, I ended up moving my Secret Base because I got sick of having to take my Rock Smash user.