Can I manually change the kms run with certain bike/shoes?

No. As you said, you can add the activities manually. You could create a single dummy activity just to get the shoe kilometers accurate. But then your activities would be off.

Is there a possibility to manually edit kilometers run with my gear (bikes/shoes)

No, because there is no attribute in a Gear item record for starting mileage.

or is it calculated only through activities with certain gear tagged in?

The mileage on a Gear item is dynamically calculated every time you go to look at its status and statistics.

But then your activities would be off.

Not necessarily, when you can create a dummy activity of type Wingsuit Flying or Boating to add mileage onto shoes and/or a bike.

But I'm not a Wingsuit Flyer, so they would be off. :D

I saw on a Dcrainmaker video a comment that you can use a FIT editor to change the total on the device.

I have an Edge 500 and VAHR. But have not used the VAHR for any bike activites.

Looking at the Edge I found a TOTAL.FIT which contained the same milage as the shown in Gear for the bike.

Since I only have a trial version of the editor I was not able to save the changes. So I added 6 dummy activities on connect as it limited each one to 1000 miles.

I also remember on the Edge that it has an odometer for each bike profile and that you can change that in the Edge.

I don't know why Connect does not allow the use of bike profile odometer to be matched to Gear Equipment. So that would help keep different bike milage straight.

I also used the edge for a few other activities (kayaking) which I changed the type in connect after downloading it. But I see that because of the default it had credited that milage to the Bike in Gear.