well he said that it takes a couple of hours for the decker because he has several combats inside of the matrix. Explain why this isnt the case.
That's the fall-back excuse of someone who just doesn't know how the Matrix rules work. I know because it was my answer forever until about a month ago.
It's not the case because it's 100% within the GMs control how long the hacker has to do his thing. Don't want it to be long Hack session? Don't make it a complicated system. Keep it to just a Node or two, with hidden nodes, firewalls, encryption, data-bombs and roving agents being your main tools. Admittedly, we
still avoid Matrix combat, because that will slow things down, but you don't have to have IC threatening your hackers life all the time for it to be a challenging and meaningful part of your campaign. Use a poor hack job to track the PCs, or to alert meat/automated security, etc. Or if your hacker is good, let him shine - everybody enjoys a good hamstringing of the system.
Also, it helps if you have an AR focused hacker - so he's there in the meat with the players, it's easier for the GM to put pressure on him this way and it just keeps things flowing. And definitely pre-plan the Nodes so you know what rolls s/he has to make and what the thresholds and consequences of failure are, etc.
All that said, the NPC hacker is a great tool if you're not comfortable with the Matrix yet, and have a small group. I sometimes wish we only had 3 players, we have 6 and it is a lot in SR - no problem in PF, but it's a lot for SR.
also can you help on the other topics too?
I'm a first time GM and I've never played shadowrun before. First of all should I wait for fifth edition or just play 4th?
I dunno, I'd say play 4 now. It's fully developed and supplemented, and there's nothing broken with it that can't be fixed by some house-rules (which, btw, I use some optional/house-rules for the Matrix). If you have other RPGs your table plays, I could see sticking with those until 5 drops, but if you want to play SR now, play now.
What is changed in fifth edition? Also are there any places where I could find paranormal creatures? I've read through parazoology but there were only f-ed up animals. My group wants something more fantasy in the creatures. Something "Classic" like the Cyclops or Ghouls and weird stuff like Otyugh from pathfinder. Are there any forums/books where I can find stats for them (of course most of the will be prime runners or lieutenants because well you wouldn't want to fight 5 cyclops at a time 
).
And will it be a viable explanation for the appearance of these creatures that the corporations were tampering with magic trying to weaponise it and somehow this came out, or maybe they were a failed experiment for trying to create super soldiers. Also what exactly are sourcebooks? Do they contain rules or only setting?
I don't dig on the high fantasy aspect of SR all that much, so I'll leave all that to the others who've already addressed your questions.
Also I will be playing with 2/3 player characters (not sure if one of us is gonna play) should I increase their starting BP or will they be OK?
They should be fine with 400 BP, IMO. The difference between a 400 BP PC and a "prime runner" is potentially pretty small really, nothing at all like the difference between a 1st level and 10th level PC in PF, so they should do just fine.
Edit 2: also without the CR rating how do i know if the group is too weak to fight something and end up killing them?
This is the hard part no matter what kind of campaign you're running. Personally, I go by the rule of 3. Dropping or adding three dice from where your PCs are at in their primary pools will be a drop or rise in "challenge rating". If your PCs are any sort of optimized, i.e. 15 in primary pools, then an equal number of enemies throwing 15 dice will be a tough battle, could easily end with a KO'd PC or two depending on how the dice fall - and it could kill them all depending on how good your, and your PC's, tactics are. An equal number of enemies throwing 18 dice would likely end with a death or two, if not all of them. An equal number of enemies throwing 12 should challenge them, causing them to expend significant resources (grenades, medkits, spells), someone may even go down, but they should win - and live. Same number of enemies throwing 9 die may do minor damage, and should take a minor expenditure of resources, probably not gonna have anyone go down unless there's a glitch in there. An equal number of enemies throwing 6 dice will get walked over, likely costing your players nothing except an equal number of bullets.
The key part of combat though is Initiative. If you want to challenge the PCs but not kill them, I like to either have my goons spend their group EDG to go first, or give them decent (probably exceeding where their other skills are at, but oh well) Initiative potential. So, the enemies may only be rolling 9 dice to attack, but their Initiative pool will be on par with the players. Secondary to Initiative is armor, have them throwing smaller pools to attack but wearing stacked armor will 1.) possibly turn the PCs damage to Stun and 2.) probably allow them to soak enough to live til their turn - may have some heavy negative penalties from being shot, but they could still retaliate.
All the other advice given for prolonging battles is good too. Tactics, cover, space, etc. dice pool modifiers are wonderful tools. Don't remember if this was mentioned, but large numbers of weak enemies can prolong battle too. There is a limit to how many mooks your PCs can put the lights out on, the rest will get to do their thing with their crappy pools.
