Doing upper/lower together is fine at this stage. Doing a split routine is for when the workout gets long enough that the athlete is unable to give a full effort through the entire workout.
Even working the whole body each workout can be done up to three days a week. Muscles need 48 hours for recovery. (Calves and abs can be worked each day, lower back- twice a week.)
In general, free weights are better than machines since machines can lock you into a range of motion that may not suit your joints/body proportions.
The need to balance and control the weight benefits many small muscles and gives a better overall workout.
Example: A lat pulldown machine
that uses a cable is better than a fixed arc pulldown
Free weight bench press
There can be advantages to using machines.
An injury to a shoulder muscle can make bench pressing impossible but the chest muscles can be isolated by using a chest press machine.
In general though, free weights and cables are preferable to fixed arc machines.
However, at this stage, establishing the habit of lifting is the most important thing.
has an extensive directory
of exercises illustrated with small videos.