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The normal effects of reputation are described here; the differences in TTO are outlined on this page. Both factions are initially neutral (blue) towards <player> and seemingly disinterested in him. Their ships, Phoenix Marauders*, happily wander around Fields Of Opportunity nuking < & looting in v4 - Snafu> passing cargo ships without a care in the world.. also without intervention from the Teladi Union, who are seemingly unwilling or unable to do anything about it.
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Maintaining, gaining or regaining reputation with Uguras Armaments and/or the Cartel is possible but it's tricky and isn't really compatible with treating Fields Of Opportunity like other systems. Without wanting to provide too many spoilers, it is worth noting that the TTO-specific mission, 'The Rising Tide' is Uguras Armament-related so it might be worth holding off from war with UA, at least initially.
Snafu adds:
<In In v4 .00b2 pirates now /act/ like pirates: they go for the loot! In the TTO sectors this is particularly significant, as once a Phoenix (taking the time until it has all its drones back) has filled its cargo bays it will fly off to trade its loot (usually) elsewhere; either way, while it does this it won't be attacking <player> or any other ships! This makes TTO sectors less of a potential wipeout loss & more of a (admittedly dangerous) place to set up trade.>
*Phoenix /Marauders/ are currently (v4.00b2) the /only/ FIGHT ship with a cargo bay (albeit small), and can only be gained for player use by boarding (AKA capping). If you can board 1 or 2 they make excellent traders within the TTO system.They will occasionally be Fight mission targets, or can of course be captured from UA or CAR (as long as you have blue reputation, their PMs won't attack your PMs).
My current recommendation is to set a Nav Beacon (available from Equipment Dealers) in an Empty Space sector immediately /south/ of Verdant Profit & use Transfer Wares to offload the PM's cargo to a standard freighter, as the PM being a FIGHT ship will otherwise be subject to any hostile factions (eg PMC) once through the gate into Albion. The trader, however, will be relatively safe if it only flies to the Empty Space sector for transfer, then back or on again to wherever it wants to trade. For a good profit & a guarantee of Teladi trade/mine ship building availability load up the PM with Scanning Arrays & trickle them in to the shipyard as needed.
Phoenix is a confusing ship classification. The ones built by the Teladi shipyards do not have the cargo space (but do have higher other specs), but a capped PM or self-built plain P both show up as 'Phoenix' when player-owned. In addition, the game itself is inconsistent in its naming: in some areas (menus etc) the ship name may be 'Marauder Phoenix; in others it will be 'Phoenix Marauder' 
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