Baffins' assistant manager Thompson has been placed in charge for the club's past four competitive fixtures with boss Shaun Wilkinson slapped with a four-game stadium ban.
Rovers continued their good start to the campaign despite the absence of their manager, with efforts Billy Connor, Tommy Scutt and an own-goal from Patrick McKay firing the visitors to a second win on the spin at Bournemouth.
Now Thompson will hand match-day responsibilities back to boss Wilkinson - and the assistant manager is hoping the team can carry on their good early season form on his return.
Thompson said: ‘He’s (Shaun) back Wednesday so I’ve already been winding him up saying, ‘there’s no pressure now, it’s over to him on Wednesday’.
‘He’s chomping at the bit to get back, he’s not been involved in anything we’ve done (on a match-day) since November.
‘He’s been heavily involved in training and I speak to him more than I do my missus! He’s on the phone everyday and on match-days.
‘It’ll be good to have him back, he’s a character as well, the lads respond to him so it’ll be nice to have him back in the changing room and hopefully we can kick on from the good start we’ve had.’
Connor struck on 13 minutes to hand Baffins a slender one-goal half time advantage.
McKay could only turn Miles Everett's cross into his own net just before the hour as the visitors went 2-0 ahead.
There was still time for Scutt to rifle into the top corner 15 minutes from the end before captain Cowan rounded off the scoring in stoppage-time.
And Thompson praised the professional performance the visitors put on.
He said: ‘It’s never an easy place to go, Bournemouth. It’s one of them grounds, it’s not the best ground or pitch in the world, so it’s all about and approaching the game as professional as possible, really.
‘We always targeted the Fareham and the Bournemouth game - if we got four points from them - and the FA Cup win away at Tadley - it’s been a good start to the season. Four points from our opening two league games is a good return, really.’