Can I drill extra holes in entrance panel
It should not be a problem making a new hole for the service cable, but you should check you local codes. Where you make the hole depends on other factors, that a licensed electrician would know. This is done with a Knockout punch, not a hole saw. If you try to use a hole saw, you will only make a mess of it. A good set of KO punches are expensive. You can get cheaper sets, that will work a few times before they get dull such as this one or maybe you can borrow one. If you need to go from 3" to 2-1/2" then you may be able to use a doughnut (if code allows it!) reducing washer.

This is quite an ambitious job for a newbie! I suggest you hire an electrician. You can not just add a bigger panel to the service, the lines at the house drop need to be sized bigger and possibly the lines to the house from the utility. You will need to change the wires from the meter, and then you can go through the back of the panel and forget about the KO hole. There will undoubtedly be code upgrades like grounding, that need to be implemented as well. And then there is a final inspection, and yes you need it, if you want your insurance to pay off in the event of a disaster. 

Putting all the Romex wiring through one hole is not acceptable. You can put as many as two through an approved (for two Romex cables) type connector. Also "bundling" of cable has restrictions as well, usually only 2' at a point. Romex must be stapled before entering the box (usually within 12"). Again, You need to find the NEC (US) code and local code requirements.

If you still are thinking of doing this yourself, I would apply to your town hall for an electrical pre-inspection. An inspector will come to your house and you can lay your plan out to him. He will tell you if things need to be done different. You as a homeowner can file to do electrical work on Your own home. After the work is done the inspector will return and hopefully give you an approval. Nice and legal, and your insurance co. will accept it!

EDIT:
Here is another cheap KO set with smaller sizes. Note that electrical hole sizes are not dimensional, such as a 1/2" electrical KO is actually a 7/8" hole, and takes a 3/8" Romex connector!

EDIT2:
It may be possible to use a junction box and a raceway to the new panel. A raceway can be say a 3" conduit connecting the two, or an approved raceway. The splices would be made inside the Jbox to single conductors going through the raceway into the new panel. You could ask for a pre-inspection meeting to see if your inspector will accept this. If not he may offer other solutions. It is hard to evaluate your situation without seeing the whole picture.