Placing component vertically in ISIS
Proteus ISIS is a schematic capture tool. It therefore does not care much about vertical or horizontal position of an individual component (assuming you mean vertical as in standing up from the board).

There are two possible interpretations of your question, I will address each one. 


If you mean the rotation of the capacitor and its leads in the schematic itself, i.e. in ISIS as the question states, then simply use the numeric keypad plus or minus keys to rotate the component after you see the green ghosted outline, prior to placement. If a part is already placed on the schematic, you can select it (click on any edge) and press + or - to rotate it, as well.
If you are looking at physical placement of a component in 3-D on a PCB layout, i.e. in ARES, and if you mean that there is insufficient vertical room above the PCB, hence the need to place the part horizontally, then you need to select the appropriate package / footprint if you can find one online. 




If not, follow the steps below to roll your own:


Make a fresh PCB layout project. 
In the PCB layout tab, Top Copper layer, add the footprints for the leads of the capacitor
In the Top Silk layer add the correctly sized rectangular outline of how you expect the capacitor to be placed on the PCB:

In my example above, the pads are 200 mil (200th) apart, and the capacitor can is of 400 mil diameter (200 mil radius) and 600 mil tall.
Now select all, right click, "Make Package", give it an unique name
Use that name to assign a package to your capacitor in your board layout, and you should be good.




Optional steps if you need a proper 3-D visualization of the capacitor:


In the Make Package dialog above, click the 3D Visualization tab, and add the following:


  TYPE=AXIALCYLINDER
  PINTYPE=BENTWIRE
  MAXHEIGHT=410th
  Y=400th
  X=100th
  ANGLE=90
  RADIUS=200th,200th,20th,20th
  COLOUR=(0,120,255)
  LENGTH=600th  



Edit the LENGTH, RADIUS and other parameters to suit the specific dimensions of your capacitor.
On a board visualization, your new horizontally mounted radial capacitor should now look like this:

Add polarity and value indicators to taste, and you're all set.