The mortar has two goals: provide support and to level (if required). If the floor isn't flat, then one or more of the legs may not set on the floor. If the tub is properly supported, that should be okay.
The tub must be set in the wet mortar. There are several things that can be used, but straight portland cement is not one of them! You can use a sand mix (aka deck mud - the mix that is used to make a shower base) which is mostly sand with some portland cement (a 3-5:1 sand to cement mix). This will not be runny...mix it until a clump holds together when squeezed together by hand, it should not be dripping wet - you just want to get all of the sand and cement mixed well then wetted (i.e., damp). It will be sort of like wet beach sand.
You can also use plaster of paris, but mixing up a big batch and laying it out before it starts to harden can be tricky - it starts to set quickly.
Some prefer structolite.
When setting the tub, you want to settle it down in the mortar until it is level. If you ledgers are set properly and the lip is not warped, you can push it down until the lip hits the ledgers.
You can, but it isn't necessary, also put a sheet of plastic right under the tub. It will make it easier to take out if desired, at some later date. It's not there to bond the tub to the floor, but to support it. Over a wood subfloor, you absolutely do want something to prevent the wood from sucking the moisture out of the mix.