That I understand, but would like to select a planet that may have older ships around it and upgrade them individually without having to pop them out of orbit.
Select the ship you want to upgrade, then press the D key. This will bring up the Details page for that ship.
Also is there a galactopedia in game?
No, we only have one for outside the game. It also only allows you to take a look at the tech trees, planetary improvements, starbase modules, and ship components. If you have questions regarding game mechanics, then you are better off either going to the GalCiv wiki or asking on the forums.
I wanted to see if there was a formula for mining resources. What I mean is, if I am mining a military resource and I have the mining at 34 on that resource what is the benefit to weapons and defense it provides when building ships? Where can I find information like this?
Mining resources increase your racial ability of the same name (Morale resources increase your Morale ability, Economic resources increase your Economics ability, etc.). The only exception is the Military resource which increases both your Weapons and Defense ability. Your racial abilities work empire-wide, so it doesn't matter when your ship has been build. The calculation is also pretty simple for weapons, defenses, and hit points, as it is just a percentage-increase.
For example, you've built a frigate with a beam attack of 10. Later on, you begin mining a Military resource, which increases your Weapons ability from 0% to 34%. This will increase your ship's beam attack from 10 to 13. Some time later, you've managed to increase your Weapons ability to 59%. Your ship, if it is still alive, will now have a beam attack of 15.
One last question, I know my survey ships gather stuff to improve my empire, +1% to upgrading, +1% to diplomacy and others. Is there a screen that shows what I have gathered to improve my empire (to date) and a with and without so I can see what it would have been if I never used survey ships.
Anomalies, just like mining resources, increase your racial abilities (though there are a few exceptions, which will provide you money, research, or improve your survey ship). You can see them under 'Abilities' on the Stats & Graphs tab of the Civilization Manager. However, you can only see the total amount you have. Seeing how your abilities have changed due to anomalies isn't possible, though in some cases you can guess it.
Is there a cap on these percentages?
Yes and no. While, in theory, there is no cap on how high your abilities can go, there is a limit on their sources. Some abilities also have a limit to their effects. Sensors, for example, are limited to 15pc. You can also have only 12 Trade Routes. Those limitations are hardcoded.
How or where can I see what they do?
Most of the abilities work under the hood. So you can't easily tell, if they have any effect. Others, however, are actively shown in tooltips. This is mostly the case for your Morale and Influence abilities. If you mouse over the Influence and Approval values in your Colony Management screen, it will tell you how much those abilities contribute.
Well, I hope this answers most of your questions.