what control do i use to set waypoints

and how do i choose what ship "appears" on the bottom display when i select a hotkey group, i want it to jump to a certain capital so i can use the abilities quickly but it always goes to some other ship

When a ship is selected and you right click somewhere, it moves there right?  So, if hold shift and right click in succession several places, the ship will move to those places in the order you clicked on them...for example, if you select a scout ships, and right click around the edge of a gravity well while holding shift, you can get a the ship to go around in circles...

Holding shift doesn't just apply to movement, it applies to any orders...you can select all your SC, hold shift, and right click on every enemy ogrov one by one so that you can quickly tell your SC to wipe out those ogrovs before they destroy your starbase...

If we're talking about waypoints as specific locations...when a planet is selected, there is a button you can click on called "set rally point"...it's at the bottom right where ability buttons normally appear, and its sort of like a yellow circle with yellow arrows in it...you can click that button, then click on another planet or object (like a structure or ship)...this will cause all ships produced at your planet to go to the rally point...if the rally point is a ship, and that ship moves to another planet, your ships should still try to rally with it (never done it myself though, just know it can be done, so unsure about that)...be careful with this though...you can select faraway planets, but you can't (as far as I know) control the route ships take to get there...when you click the "set rally point" and then click on where you want that point to be, phase lanes should light up yellow showing how ships will get to the rally point...just make sure that route doesn't go through enemy territory or the pirate base...

Sorry did see this when I made my last post...I'm assuming when you say hotkey group you mean like a fleet, right?  The ship shown at the bottom is always the fleet's flagship...in fact, when you look at the empire tree on the left, any fleet's flagship with have a small white triangle in an upper corner of its icon (not too be confused with a ^ or +, which means ability or SC slots are available, respectively)...

I don't know how to set a specific ship to a flagship, but I know that if you zoom out, select all ships in the gravity well by clicking the black bar to the left of the planet, and make a fleet this way, the highest level capital ship will always be the flagship...

When you select a group of ships, 1 will have a slightly whiter box, thats the flag ship. Use tab to cycle through until you are on the one you want. I think shift + tab cycle backwards or ctrl + tab not sure.

how do i tell the amount of fleet supply im using up?

Mouseover the fleet supply box will tell you.

[_]-Greyfox

when should i start building starbases?

In general, starbases should be used when either 1) You know your fleet cannot successful defend a gravity well or 2) If you move your fleet, you know an enemy fleet will attack an undefended world of yours...

For the first situation, this usually occurs when you play the AI on higher difficulty levels and/or pirates are active...in multiplayer, this would occur if two players are merging their fleets and attacking one player....

For the second situation, this usually occurs if your empire consists of multiple "fronts" and moving your fleet to one front leaves the other vulnerable...in most games, all players are positioned around the star in a system, so most players usually have two fronts, one on each side...in single player, it is a good idea to build a starbase or two on the front that is easiest to defend (has the least amount of chokepoints) and have your fleet go on the offensive on the front that is hardest to defend (is open and has many ckokepoints)...

In multiplayer, things can be much different because humans are smart...they'll realize you're building a starbase and shoot it down before you can finish constructing it, or they'll just sit there in your gravity well with a bunch of bombers, or they'll just go around or attack a different planet...starbases are expensive, and building them too early comes at great sacrifice to your fleet, so be careful...

In general, I'd say don't build a starbase unless you are unable to go on the offensive or your fleet is constantly moving around, trying to defend too many positions at once...

is it worth it to explore most planets?

Well, it depends...in MP games, no it's usually not...

In single player, if you are on a very large map and have taken over a large portion of planets, you're odds of finding something are pretty good...

You should only invest in exploring planets if you are in a stalemate that heavily favors you defensively or if you have more resources than you know what to do with...

As Advent, make sure to research the tech that reduces the cost of exploration before doing so...

It's a gamble; you might find something awesome, you might not find anything at all.  Usually it's only worthwhile later on when you're swimming in money from a well-developed economy.  Most games, I don't do this.  Sure, I might have a nice artifact, but most of the time I get a consolation prize that isn't worth the cost of searching.

do iconus guardians' shield projection stack in shield strength?

No they do not....however, the ability is only good as long as the iconus guardian don't run out of shields...if you like the iconus guardian, I highly recommend having a progenitor with shield regeneration...iconus guardians recharge their shields very slowly, so without a progenitor that can be nearly useless after one or two battles...

More like ten seconds into the first battle...

im still having troubles with hotkeys,

i got a halcyon, selected it, and hit ctrl+1 to make a group

later i added some illuminators by shift-clicking them and hitting ctrl+1 again, then when i press 1 to jump to my group,

i get an illuminator's stats in the bottom bar and hear its voice. i want it to select the carrier on the bottom bar when i press 1

ive tried everything, taking them out of the group and putting them back in, creating and leaving a fleet, it still goes to an illuminator.

and on an unrelated note, is there any way to reduce fleet upkeep cost